Me too....what am I doing wrong....

I can't explain what you experienced with the flash, and I'm unable to duplicate it on my end. The flash should never pop-up automatically while in Manual; you have to press the flash button, located near the lens mount just above the lens release. If it was flashing during autofocus, that would have been for AF-assist. If it was flashing during exposure, and the EXIF data are wrong (unlikely), then the lens may have been blocking the flash output to the subject.

To verify the advice I'm giving might actually work using the built-in flash with a 100mm macro, I tried to somewhat duplicate your equipment setup and workflow. I put a 20mm extention tube on my cheapo Canon 28-105mm zoom, which gave me about 1:2 magnification with the subject just under 4" away from the lens, and used the built-in flash to take some snapshots of whatever bugs I could find within 6 feet of my back door. Picked three images, did RAW conversions to jpeg with BreezeBrowser using default settings, and resized to 1000px... with PhotoScape :-).

Results, with full EXIF data attached, are here, here and here.

You need flash because the small aperture required to get a reasonble depth of field would otherwise require a very long shutter speed to obtain proper exposure. What we are working towards is an image that is completely illuminated by flash.

Some side notes:

PhotoScape's RAW converter produces awful results with my 30D images, has absolutely no options available (sorry, "halfsize" and two broken white balance settings don't count as options), and only writes jpeg files. Don't ever use it to work with RAW-formatted files.

I know I'm lazy, but I almost forgot how much of a pain in the ass it is to use a short lens for macro work in the field! The guys who talk about not wanting to use a long lens and be impeded by dragging a tripod around while chasing bugs probably don't realize there is no chasing involved with a long lens. I was shooting butterflies last weekend at 180mm+2X from over 6 feet away while sitting on a foot-stool, and actually had to back up a couple times. Wasps, hornets and bees from 2-3 feet away while sitting on the ground. But today I had bald-faced hornets landing on my hands and face while trying to shoot from a few inches away.

Can't hide anything from you....
I use the software that came with the camera to do cropping or any editing but I use Photoscape to resize. I guess I just like it. Currently I'm not shooting RAW (might get arrested), just jpegs so there's no RAW to jpeg conversion going on.

Also, I just want to say that I really appreciate you taking the time to help me. I just hope that I can repay you with some good critter pictures. I don't have any money....spent it on equipment. Anyway, I just wanted to say thanks.

Oh, and by the way, you really suck for being able to just go out and click off great pictures without even trying. Maybe someday I'll get there.

Hopefully by now you noticed at least two things about those photos:

1.) As the file names will point out, I didn't shoot three photos, I chose three photos. I probably shot around 40-45. Most of the rest were out of focus, improperly exposed, did not properly show the subject I was trying to photograph, etc. If an Ivory-billed Woodpecker landed in front of me, and all I could manage were a dozen blurry images, I would delete them all.

2.) Note the settings I used for the spider photo. I set the flash exposure compensation to 1 2/3 to account for the bright surface that occupies most of the photo.

I see the flash exposure and I'll work on it.

I also take many many pics and select the best of each critter out of those to crop or whatever and put them in a different directory. Then, if I have multiples of a given critter, I go through those and pick the best of those after editing and that's what I upload. My problem though is that I'm obviously not a skilled photographer so a lot of the images aren't the quality that I want them to be (and BugGuide wants them to be). I need to learn what each "custom" setting means and what it will do when I change it. Mainly I just use the full auto or the "macro" auto and let the camera do most of the required adjusting. But, as you and others have pointed out, I need to learn the manual side of it much better.
Work in progress....

I'm an idiot... or rude, maybe forgetful, but I didn't supply links with those three images I posted so you could actually see the original uploaded file.

I went back and edited them, and added a link in the body of each.

Thanks for the links.

Ok, here is my first attempt at RAW : here and here and here and here. Let me know what you think.

These were done using your suggested settings, modified, and with the flash turned ON.
It was late in the evening yesterday with fading sunlight. At first the images were dark again, even with the flash, so I tried adjusting the ISO but that didn't help much. I finally set the ISO to 100 then adjusted down to f7.1.
Here's what I've learned :
I learned how adjusting the fstop affects light and dark.
I learned that manual focus most times yields better results than auto.
I learned that a faster shutter speed is much more preferable to auto for macro.
I learned some on how to manipulate RAW files.
I learned that I really like the RAW format.
I don't like the fact that I can take less RAW images than JPEG due to file size.
I don't like the fact that the RAW images have to be converted to JPEG.
I also learned, and saw, the difference between RAW and JPEG and how much clarity and detail is actually lost in a JPEG. It's pretty astounding!

Do I completely understand what I've learned and how to apply it from now on?....not even close....yet.

It's amazing to me how you can see every little hair and the detail is awesome!

Those are much, much better!

I wouldn't expect an increase in quality just from shooting RAW, but then I don't know the sharpness settings in your camera. I think I remember a review that slammed one of the Canon DSLRs for using aggressive default sharpness settings. With RAW files, those camera settings (color, contrast, sharpness, white balance, curves, hue, color temp, color space) don't affect the actual image data contained in the file, only the EXIF tag information used to describe it.

I'm confused why you are unable to use a smaller f-stop. If you are limited by the amount of output your flash is able to provide at ISO 100 and f/7.1, you should get a similar exposure at ISO 200 and f/10, and with ISO 400 and f/14.

Anyway, NICE WORK! Keep banging away at it and you'll figure these things out.

I've still got a long way to go and a lot more to learn and figure out but you've given me a good jump start.
One thing I've figured out is that I need to get a new monopod. I had to tear up the one I had because the bolt in the end that screws into the camera stripped inside the monopod and I couldn't get it loose from the camera....my new camera! So, I had to perform surgery not long after I got my new camera. Not something I want to do again. I had to use a knife, a hacksaw, and vise grips (on the monopod) but I finally got it loose. I haven't had a monopod since because I'm afraid to screw anything into the camera again. But, it wasn't the camera, it was the cheap monopod. I need to get a new one though because I shake like a dog crapping peach seeds and I know it's affecting the pics.

The Lighty Pod looks nice, but you're right Ron, that name has to go!

I have a Bogen monopod, I think it's this one, that I don't use much anymore. The pistol-grip is very nice; I don't think it's ever slipped on me. The twist-lock section is annoying though. Too loose and it slips. Twist it too tight and it tends to jam.

I recommend, at a bare minimum, that you get something with a removable head that also supports quick-release plates. The Bogen/Manfrotto "RC2 System" plates are pretty popular and inexpensive. The Arca-Swiss system (or "Arca-style") is a bit more expensive and IMO much more secure. In either system, the quick-release plates attach directly to your camera or lens, and you LEAVE them there. Then you simply attach the camera/plate to the quick-release clamp on the tripod head.

Sam, send me an e-mail. I need to mail you some stuff.

I sent the email like you asked. Did you get it ?

Just responded...

I have a Slik Lighty Pod II, which is fine if you can get past the name. (I think they're up to III now.) It's fairly inexpensive and included ball head. Try Adorama. Ritz has an OK alternative, but it has those twist-lock legs, which I don't like.

that jpeg has a somewhat destructive compression method. Everytime a jpeg file is saved again (after making alterations), pixels may change to conform to neighboring pixels. Eventually detail is lost and parts of the image become "moth-eaten" or "water-marked." This effect increases with every save.

I warn people receiving jpegs to immediately save it to another format (I prefer tiff) before making changes or setting up for publication use.

My routine is have the camera save RAW, download and convert to tiff, edit and make minor corrections then save as psd (PhotoShop). Saving as tiff would be a good route if the file sizes (big) can be delt with. Jpegs are used only when needed for previews, Powerpoint inclusion, or most important "BugGuide!"

Just a suggestion, it's disappointing to see a good shot looking chewed up, more disappointing to have to correct the image before publication.

These are camera-specific books that, for me anyway, are much clearer and better organized than the camera company's manuals. I find them particularly useful for figuring out custom settings. Often, the author will make suggestiong on what to change and what to leave as is. If one of these books is available for your camera, see if you can give one a read at a bookstore before purchase. Bet you'll find it useful!

but the flash was "flashing". I know that the exif says it's not on but it flashed. It wouldn't "pop-up" automatically but once it was up it was flashing. I don't know what's up with that....at least something looked like it was flashing....maybe I was having some sort of fit but there was something flashing....really....
Also, I took these this morning with plenty of light outside. Why would it need flash in the first place ?

And no, the pics haven't been altered in any way except I sized them down for upload but other than that this is exactly how they came out of the camera. I didn't want to do anything to them so that you could see exactly what I'm getting.

if your camera uses a focus assist light, on auto focus, what appears to be a "flash" will be noticed in some situations. Just a thought.