I also noticed the same problem today. To be able to see where the
invisible pointer was, I activated the option "Locate pointer" in the
Mouse Preferences (the one that shows the position of the mouse when
Control key is pressed).

Then, by chance, I did something that brought the pointer back: with the
help of the Ctrl key, I used the (invisible) mouse to resize a column in
the package list in Synaptic. The pointer changed shape to the resizing
arrows, and when I released it, it got back its arrow shape. I wonder if
resizing anything would make the pointer appear again.

-- 
[Jaunty] No mouse after login in Ubuntu after install of Ubuntu-X ppa package 
today
https://bugs.launchpad.net/bugs/455603
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