[James Stanek]

I think the flicker you are seeing is not unique to the 7D, but is typical of most DSLRs when used for timelapse or stop motion work. I chased this problem around on several Nikon bodies, and since then, I’ve seen confirmation in several timelapse oriented website discussion groups. The flickering is caused by the iris. On modern DSLRs and SLRs, you may set the iris manually, but the camera will open it all the way between shots, so you get the brightest viewfinder to see through (and for the autofocus system) while composing. Then, when you press the button to take a picture, the mirror swings up, the camera stops the iris down to the selected f-stop, and the shutter activates.
The problem for stop motion work is that the iris never stops down to the exact same place twice. This error is well within the tolerance of what is needed for still photography, which is what the camera is built for. However, when you play the frames in sequence, your (very sensitive) eye sees this tiny variance in exposure as flicker.
Regardless, it’s relatively easy to determine if this is your problem. Make a series of tests at different f-stop settings. The problem should go away when the lens is set to it’s maximum aperture. It should get progressively worse as you stop the lens down further towards F/16.
Fixing it is harder. You can shoot wide open all the time, which limits depth of field and generally requires NDs for adjusting exposure time. You can shoot nearly wide open to minimize the problem and live with it. You can try one of the various flicker correction plug-ins. Personally, I haven’t had much luck with the plug-ins, but I haven’t tried the newer ones. Try checking out some timelapse on DSLR forums for more info. I only periodically skim them myself, so I don’t have any particular ones to rec.