I'm pretty sure this isn't about the mouse not moving, or about Logitech
hardware specifically. I get a very similar problem but the symptoms
I've noted are a bit different. Luckily I can reproduce this case all
the time on my 11.04 box:

 - Click on the power button icon, select System Settings
 - The window appears with the various options laid out in a grid. I click 
'Appearance'.
 - Appearance app opens up, in front of System Settings app, as expected.
 - When I click on the Appearance app, the mouse clicks go THROUGH that app and 
click on what is behind it.
 - This way, I can launch other apps within the System Settings window even 
when clicking directly on the Appearance window.
 - I can continue to click on things in the System Settings window through 
whichever new windows appear, if I know where on the screen below the top-most 
window they are located.

So it's not that the mouse pointer is stuck, it's that the clicks are
going to the wrong window entirely. The mouse position is reflected
correctly however.

This happens for me with both of the mice I have tried in the months
that I have had this problem (a Razer Diamondback and now a Cyborg
R.A.T. 5 mouse). Both work fine on Windows XP, Vista, and 7. Both are
USB and wired. And both work fine in Ubuntu up to the point where this
issue appears.

I sometimes have another pointing device attached (USB Wacom tablet) but
I made sure that was disconnected today and still the problem appears.

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https://bugs.launchpad.net/bugs/375905

Title:
  Mouse focus gets stuck over control objects

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