As far as I understand, its probably a video card issue?
I guess it's not, as other user confirmed this when having 5:4 resolution set in settings file. I think there is something wrong with layers where these black bars are being applied.
The possible workaround is to use 1280x960 and activate image centering via GPU, both ATI and NVIDIA can do it AFAIK. But it doesn't work well for some games, and i didn't test it with Aquaria yet. If it works via GPU, then it will result in absolutely same visual resolution for 5:4 monitor (as if someone would use native in-game 1280x1024 resolution), but without those glitches.
And if that was about vsync - i don't know. Just remember that someone on the board was talking about this issue for ATI cards with Vista OS. I'll try to update drivers, but i doubt it will help.
