I've actually had issues with that resolution - when I try to use desktop height and width, it's like it doesn't return to correct resolution - I have to hard-code it instead. Works fine on my main PC, but when I work on my netbook with that res I get these same issues.
It looks to me like the screen is being scaled weirdly, so losing whole strips of pixels, maybe even having to downscale the image to the window - typically an upscale is obvious because you'll get blurring. I think the desktop height and width check is returning a resolution bigger than the actual screem, and the re-scaling is causing these issues.
Try specifying the resolution instead of checking the desktop res, I'm sure that'll 'fix' it.
