Somehow I got sucked in to investigating this.. It definitely happens to me too.. AMD Radeon 6800 if it helps..
I started playing around.. and this thing makes no sense..
I deleted everything from wertandrew's project except debugbox (sprite), limelight font (spritefont), and the playerwindows (sprite) (-- no 9-patches left!) and the bug is still there.
Deleting either the debugbox or the spritefont makes it go away.
OR
Taking the set color effect off of either of them makes it go away.
OR
Adding another effect to either of them also makes it go away.
So anyway.. not sure I've helped any, but it seems to me the 9-patch is irrelevant.. If it might help, here's the capx super simplified (no 9-patch) and still bugged: [link removed in lieu of new one]
EDIT: I just reopened that file and now it's not bugged.. so maybe it only stayed bugged after deleting all the stuff..
EDIT again: I went through my delete objects test again, but this time I left one more spritefont in.. the saved file still contains the bug (super simplified, no 9-patches). the "makes it go away" list above still applies, except that when deleting the playerfont spritefont, you don't see that it's fixed until you save and reload.. so confusing.
Here it is: https://drive.google.com/open?id=0B1Aaz ... UdBVEZxM2s