I'm encountering the same situation using metacity-2.4.55-6 on
Redhat Enterprise Linux 3. I have a couple of additional observations:

* I agree that it happens when you click on an already-focused
  window and try to drag. It sometimes gets "unstuck" after a 
  few seconds; more often you have to click a second time and the
  window jumps there.
* (Important clue) It doesn't seem to happen with GTK apps, but 
  does with nedit (Xt/Motif based), xclock, a minimial Motif
  app I wrote, and my large Xt/Motif-based software package. 
  GTK apps like gedit, gnome-terminal, etc., don't exhibit this
  behavior. I've looked at xprop output trying to narrow the
  differences in  WM_HINTS and other atoms, but haven't been 
  able to see any pattern. It also fails with "K" apps (Qt)
  like kedit. 
* Sometimes the condition becomes "cured" during a session. I 
  haven't been able to narrow down a trigger (looking at 
  .xsession-errors).

Is this some kind of session management issue?
