I have had a hard time with erratic mouse behaviour in eclipse Galileo (Build M20090917-0800). Most of the time in dialogs moving the mouse over buttons would focus and press them them but due to that left click did not do anything.
I found an easy solution here: run eclipse from a shell-script:
#!/bin/sh export GDK_NATIVE_WINDOWS=1 /home/[your eclipse directory]/eclipse
export GDK_NATIVE_WINDOWS=1 did the trick for me!
Update 2009-11-17 when Eclipse restarts itself the setting gets lots so I close/start eclipse instead of using the restart function