I have the exact same, annoying (how small is enough?) issue.

In my case, I use a laptop 1280x800 screen together with a 1280x1024
desktop screen.

There's this forum post where you can the issue is discussed as well, though 
there's not much useful info there:
http://ubuntuforums.org/showthread.php?t=1170588

This issue is could very well be encountered the first time you boot a
new Ubuntu installation if you have both screens plugged.

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Mouse disappears into dead area when using asymmetrical dual screen
https://bugs.launchpad.net/bugs/387795
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