I have an ATI (native Xorg) driver on a Radeon 9200 card set up with 2 screens as non-rectangular, merged xinerama, with an offset specified.

When an application goes into fullscreen (which is usually undesirable since very few applications bother to correctly identify the xinerama screen and so place themselves over the centre of the 2 screens somewhere), and then switches back out of fullscreen, it leaves various things in very weird states (I'll get to describing them).

Relevant xorg.conf settings:
MergedFB true
MergedXinerama true
MergedNonRectangular true
CRT2Position "Rightof 150"
MetaModes "1280x1024-1024x768   ...."

Screen 0 is LCD - 1 is CRT.

Definition of weird:
Screen 0 is left with some 'no-go' zones for the mouse, but looks ok - size has been restored correctly.  The bottom 1/4 of the screen is no-go, and a small square in the top-right of the screen is also no-go.

Screen 1 is in the correct resloution, but is suddenly got a larger virtual vertical resolution - and so scrolls.  However apps like the 'kicker' which hug the bottom of the screen, are still left where the screen should be finishing - and not at the new 'virtual' bottom of the screen.

I've also noticed (possibly unrelated, but happened about the same time - don't ask me what version - 7.1, but other than that *shrug*) that when the rhs kicker pannel is on the top of the screen and is scrolled away, then I can't drag apps in the LHS screen applications past the top of the RHS screen - even though maximising them works ok. Yakuake also drops down from the wrong spot in the lhs screen.  This could be a kde problem - but I'm including it here for completeness.

Other than that - my Xorg 7.1 is debian package 7.1.0-11
Kernel is 2.6.17 Beyond-4.