My windows inside Eudora were disappearing, and it seemed to make no sense - I'd summon one of the mailboxes from the list, move the mouse over, and *poof*, it would just disappear (but still be listed as open). Very bizarre. I couldn't get the windows to "stick", even after closing and reopening Eudora multiple times. Then I got myself into a very bad situation by telling it to float the mailbox window - and watching that one disappear.
This looked very bad. Then I moved the mouse to another app, and noticed that Windows thought that the center button was down. No amount of toggling fixed that - Windows was just in a bad state. Finally, I rebooted to clear that, and all was well. Really, really weird.