I had a similar problem last week (maybe the same?). I bought a new
mouse 3 weeks ago (logitech usb and wired) that worked nice since then.

Tried with a different login : same problem.
Removed the nvidia proprietary driver, and used the nouveau driver : same 
problem (+ some refresh problems during scrolling)
Pluging and unpluging the mouse didn't solve the problem. The computer was 
almost unusable without keyboard navigation skills (which isn't the case for 
everybody at home).

Note : in Rhythmbox, when the problem occured and the mouse focus was
grabed in the list of songs, I saw sometimes the color of the selected
song switching to grey during 1 or 2 seconds without doing anything.

With another mouse : same problem
Booting from a USB disk with maverick 32bits (instead of AMD64) : same problem.

Then I remembered there was some parameters in the BIOS concerning USB
mouse and keyboard support. My previous mouse was a PS2 one, and my
keyboard is still a PS2 one. So these parameters were disabled in the
BIOS.

For completness and because some actions may have had an influence in the 
result (maybe some cold reboot or disabling/re-enabling USB could have 
correctly reseted the hardware), here are the details of what I did :
1 - I first enabled only the mouse parameter (since my keyboard is PS2) and did 
a warm reboot. The problem seemed to disappear. But few hours later my wife had 
once the problem.
2 - I completly shut down the computer to do a cold boot.
3 - I disabled USB in the BIOS and rebooted until login (so no mouse, just PS2 
keyboard),
4 - then rebooted into the BIOS, only enabled USB 1.1, enabled both mouse and 
keyboard USB support, rebooted and played a while to check everything was okay 
in a session,
5 - then rebooted into the BIOS, re-enabled USB2, rebooted and since then I 
don't have anymore problems with the mouse.

I don't know why the new mouse worked few weeks with these parameters
disabled???

Hope this can help.
PS : Same bug seems to be related in 375905

-- 
Mouse clicks stop working sporadically
https://bugs.launchpad.net/bugs/41301
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