When I raise or lower a window, the window does not appear to move. However, the
mouse behaves as if the raise/lower worked. Here's an example. I have two
windows, A and B on an Xnest display. A overlaps B some (and is on top of B). I
raise B (e.g., by clicking on its titlebar in most window managers). Nothing
visible happens, which is unexpected. When I click the mouse in the area where A
and B overlap, B now gets the clicks, even though A (still) appears to be the
top window. I have focus-follows-mouse set, so the keyboard focus also changes
to B in the overlapped area. Lower has the same effect.

This happens with twm, fvwm2, and kwin.

I've found some things that temporarily synch it (i.e., set the visible stacking
order to match how I set it):

1. creating a new window (e.g., starting a new X client)
2. Sometimes, bringing up a root menu in twm and fvwm2
3. Bringing up the window-specific menu in kwin (middle-mouse on titlebar)
4. Quitting the window manager

2 and 3 may just be instances of 1, I don't know. 

This did not happen with 6.8.0.

FWIW, it also happens with the Fedora 3 Core patched 6.8.1.