I have the same problem using Ubuntu 10.04 desktop (64 bits). No propietary 
drivers are in use on my system.
Cursor goes invisible almost certainly shortly after I use Remote Desktop 
Viewer to log into and operate remote Ubuntu machines. Regardless of how long I 
have been using the system, it's only minutes or some times after I start using 
the Remote Desktop Viewer that my mouse goes invisible.

The dmesg I see (though not sure it's definitely related): 
[ 8572.514292] [drm] nouveau 0000:01:00.0: EvoCh 0 Mthd 0x0000 Data 0x00000400 
(0x0002 0x01)

The workaround I've used is to turn on "Show position of pointer when
the Control key is pressed" in System->Preferences->Mouse. By doing that
I can see where the mouse is by pressing the Control key repeatedly
whenever I need to use the pointer. It's annoying though, and I lose
copy/paste functionality (Ctrl-C and Ctrl-V) with some applications, so
I usually have to reboot after this happens.

Have been using the Remote Desktop Viewer for several months now, and
never had this problem before, started happening only about a couple of
weeks ago.

Have had Ubuntu desktop 10.04 64 bits installed here for about a year.
Before that I used Ubuntu desktop 32 bits (also 10.04) for several
years, never had this problem before. I use Ubuntu 10.04 (32 bits) at
work, and I use Remote Desktop Viewer there frequently, have never seen
this problem there either.

The output of uname -a on my 64 bit desktop where I'm having this problem:
Linux raul-desktop 2.6.32-41-generic #91-Ubuntu SMP Wed Jun 13 11:43:55 UTC 
2012 x86_64 GNU/Linux

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https://bugs.launchpad.net/bugs/716147

Title:
  cursor disappears on one screen of dual monitor setup

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