I continue to have this issue occassionally with both the projection and stamp brushes. It also exports to the saved texture, it's not only seen in the viewport, and the seams seem to follow the topology of the model.
Here's an incomplete test texture I tried exporting, the seams seen are the same effect as the one occuring in the viewport, but seen in the exported texture file.
http://img31.imageshack.us/img31/6170/eyetexturelefttestpart.jpgI asked my teacher about this and he suggested that it might be an issue of graphics card compatibility. I have an ATI Radeon HD 5450 and incidentally I know that it is causing me some occasional issues with interrupted video playback and font display on Desktop icons, so it might be the reason for this as well.
I haven't updated my graphics card's driver so I don't know if that fixes this issue, my current driver version is 8.662.0.0.