With a fresh install of Natty, I often have small, invisible, seemingly-randomly-positioned mouse "dead spots", where the cursor becomes the arrow (regardless of what's underneath), and any interaction (clicks, mouse moves and scrolls) are not forwarded to the application underneath. This often results in having to move the application window to get the content I want out of the deadspot.
The dead spots are consistent between programs (currently Chromium, Netbeans 7.0, and the Ubuntu Software Center).
There is a thread on the forums of other users with similar problems, but I could not find an associated bug report.
http://ubuntuforums.org/showthread.php?t=1743026
Attempts to use ubuntu-bug with the -w option to identify one of the dead spots returns a "xprop failed to determine process ID of the window". Even when the dead spot is over an application that can otherwise be identified (i.e., repeating the ubuntu-bug -w and clicking slightly to the left of the dead-spot seems to correctly identify that I'm clicking on the Ubuntu Software Center.)
An easy way to see the effect is to open gedit (or some graphical text editor) and move the mouse over the empty document. Most of the area will show the cursor as a the "crossed capital letter I" (i.e. a T also crossed underneath), except in these "dead spots" the cursor reverts to the mouse pointer. As mentioned in the OP nothing useful can be done with mouse interaction while the mouse is in this area.
One exception to the rule that this dead spot applies to all applications is Tilda, a drop down console (quake-like), which I can easily imagine has different drawing and capture rules.
Stock Ubuntu 11.04 install on a Dell mini 10.
Additional information will be happily provided upon request.