Hi Luthyn, I've had this issue many times, and it is usually (in my case) caused by poor gridfitting—the way pixels line up with the vector points.
The solution I use is to:
Set the document units to pixels
Set the position and size of the artboard to whole units of pixels
Adjust artwork so that it aligns to the pixel grid
It helps to turn on Pixel Preview (View menu) and use the Transform Palette to check the position of objects and points. Using the Control Palette's "Align to pixel grid" option can sometimes help, but sometimes hinder, this process (probably due to my inexperience).