Bumping this, as I am having a similar issue, though the OP was a bit vague. I've been updating a single Atlas in my project for a while, and starting today began having a "jumbling" issue. The majority of my textures are PSDs, though there are a few PNGs as well.
I've done the prerequisite research, and the issue is not due to size limitation. I tried applying some of the recommended tricks for Font scrambling (resetting prefab spacing, etc.), but nothing is working.
An obvious workaround would be to create a new atlas for the images that I'm adding, but it doesn't really solve the problem, and I'd like to know definitively what is causing this to happen.
From what I can tell, every pre-existing image in the atlas has been shifted on both x and y axes by the same number of pixels (haven't determined the exact value yet).
After examining a handful of the textures, some of them appear to have borders or padding values set where they previously had none. It didn't happen to all of the textures, and I can't identify any predictable pattern.
Any insight would be greatly appreciated. As with many other users, I'm really blown away by the overall usefulness and convenience of the tool . . . thanks and kudos to ArenMook!