Yeah, almost all the firewire cameras do the auto-exposure thing. I highly recommend the fire-i, it is a great little cam.
Basically what happens is that when the cam is looking at just the screen with no blobs on it, it all has a certain average luminosity, and the auto exposure and auto brightness adjust for that (this is your background image) now, as soon as you put some blobs in the image, the average luminosity of the entire image goes up (because they are brighter than everything else) of course, if the luminisoty went up by the same amount every time, this wouldnt be an issue, but the more blobs, the more the auto-exposure change.
Now, dont get me wrong, this isnt a big change, it is a subtle one. But it is enough to make the whole system just that much less sensitive. If your entire foreground image is changing in relation to the background image, then in order to successfully find the blobs, you will have to have a higher threshold, which means that your optics (ie how much IR is shining on your surface minus however much IR is coming in from the ambient light) will have to be higher. Of course, it is a bit of a spiral, the better your blobs stand out from the background, the more the camera will auto-adjsut the exposure.
now, as i mentioned it is still a subtle change. Even with the auto-settings on, my blob detector still works fairly well, but there are more false-detections (ie detecting your palm as it hovers over the surface etc.. ) since I am doing a diffused illumination, this is kinda a big deal. If you were doing FTIR, you might not even notice the auto-settings.
The other thing to do, as you mentioned, is to use the firebrain API to adjust that stuff, thus enabling you to be able to use whichever API you wanted to capture. I avoided this route simply to try and keep the code a bit more portable. (and i was too lazy to try and find the fire-i api and get it working
All that said, i am very keen on the qtKit capture stuff. and it is a fairly easy bit of code to replace the SC stuff in my code with the qtKit stuff. Once I get all the basic bits in place (ie a working configurator for all the little bits and an event generator) then I will start adding more robustness to the code. things like the ability to use CIImages, maybe convert the blob detector so it can act as a CIImage filter, the ability to use the qtCapture if you want, all that sort of stuff.