I have a recurrent problem with the mouse not working correctly in Reader after it has been open for a while. When the problem happens, I can no longer use the mouse to select any of the Reader menus (File, Edit, etc), nor can I switch between documents by clicking on a document tab. I can still select menu items and switch between tabs by using the keyboard, and the mouse wheel still works to scroll up and down through a document. If I close and open Reader and reopen the documents, the mouse will work for a while and then give the same problem as before.
Ths problem happens on several different linux systems I've used, and has happened with multiple versions of Reader - currently using 9.4.7 on Ubuntu 10.04 amd64. No problems with using the mouse in any other application that I use.