I'm using xmonad with Gnome on Ubuntu 12.04, and when I start KeePass2, things work almost fine. If I right click on something (or left click on "File", etc), I get the popup, I edit stuff, I hit "okay" or whatever. After the menu or popup is dismissed, menus no longer appear for me. Right clicking on anything, or left-clicking File does nothing. I have to close and restart the application.
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