The Problem you are describing sounds like the problem i had. Had you been playing with the fbkeys configuration applet? to try and add shortcuts?
If so, when you hit save anything that normally happens only on 'Desktop' will happen all the time.
fbkeys has this bug where if it doesn't recognize certain functions it removes them from your ~/.fluxbox/keys file.
I had that problem then fixed it by following this forum <http://ubuntuforums.org/showthread.php?t=617812
Now i just find it easier to edit the keys menu by hand
I hope this helps
Edit: The forum I linked, is not so much as a Step by Step Fix for that, It is a really nice tutorial on how to make your 'keys' file by hand due to the buggy fbkeys...
It is really easy, if you can edit a file you can setup your own key file in minutes!