I hope you've saved the workspace as a custom workspace. What happens when you restart Photoshop and re-load the saved workspace again? Is it still messed up?
Can you try trashing prefs: http://forums.adobe.com/thread/375776
Sure, I've save the workspace before. After the restart I can reload the settings and everything looks as wanted - until the next start. I will try the pref trashing.
EDIT: I am experiencing the same beahviour on my laptop.
Yes, Trash your prefs and let us know how it goes.
Thank you for the tipps. Trashing the prefs seems to have done the trick.
EDIT: I checked and already had full rights on the relevant folders.