I am chiming in to confirm that I have the same problem using:
Ubuntu 8.10
NVidia Driver Version 177
Xorg - Xinerama

I can't use twinview as one of my displays is rotated CCW 90 degrees.
With Twinview, rotation affects both displays.

But, with one display in portrait and the other in standard configuration 
landscape, I can consistently recreate the failure by doing the following:
Using Synergy, if I move from the bottom of my client computer screen across to 
my Linux display, out of the range of my standard screen, the mouse jumps the 
middle monitor directly to the bottom of the portrait display.  Once it skips 
the main display the mouse clicks are no longer registered.  The key to failure 
on my system is to move the mouse from one display to another where the display 
area does not reach.  When working from the top of all screens there is no 
problem.

The other way to recreate failure is to allow for a long period of mouse
inactivity, and for any of the screens to sleep.

My setup worked perfectly in Hardy.  I regret updating my computer as
quickly as I did to Ibex, and likely will have to downgrade in order to
regain productivity.

-- 
X.org will stop responding to mouse clicks on Ibex with Xinerama.  Occurs 
frequently, Fatal Error.
https://bugs.launchpad.net/bugs/296167
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