This is an incredibly obscure problem and it took me ages to figure out what was happening, but I thought I'd see if anyone else has this issue: I make my images for a .GIF in Illustrator, one image per artboard. After I've got all of my images ready I use PSD to import, each to its own layer, and then make the animated .GIF from that. However, I've found that in AI if I don't have all of the artboards on the 1-row layout feature, they misalign when I import them into PSD. (Meaning, if I have four rows of 5 images each instead of one row of 20 images.)
I spent days trying to align images for an animated header I was working on and was about to give up when I tried rearranging my artboards to see if that made a difference, and it did. Has anyone else ever run into this, or know what causes it? The artboards are all exactly the same size, so that has nothing to do with it.