I don't trust Illustrator's own align to pixel grid options, they have too many side effects, consequences and quirks.
I prefer the Wundes script PixelAlign, which works more like the buttons in the Align palette - you hit it once, it does its thing, the shapes are aligned to the pixel grid once, and then nothing else happens. No surprises.
I can't guarantee it'll fix this problem, as it seems to be a strange problem that is difficult to replicate, but this is something worth trying for anyone with pixel grid problems.
Direct download link.