aryq's clue was significant and your follow up explained the problem; here's what's happening:
SC is trying to determine which backround areas of the window are (semi) transparent. Whatever this bug is that is causing the window to move during this, is making SC think there is some partial transparency over that entire area of the window, so that the text all appears as semi-transparent to SC (even though when you look at it you dont see the effect).
So when the pixelate effect occurs, its not "clearing" the transparency, and so the pixelatated regions have some partial transparency where the text was.
So here's what to do:
1. I'll consider that a bug and have pixelate always completely clear any transparency when pixelating. I'll try to have an SC update in the next week.
2. In the meantime, either fix whatever weirdness is causing the window to move, or to disable this transparency detection (which by the way will speed up capture), from here:
Let us know if that fixes it for new captures.
You could also do this for existing captures: Before applying pixelate or similar effects, choose 'Merge Background Transparency' from the objects menu. That will remove any transparency from the image.