KRAL2  I ran on the same bug.

It happen when you have applications assigned to spaces higher than 4, and DockSpaces throw away theses spaces (without any warning).

You can correct the mess editing plist files. Use Pref Setter for that task, it's very handy.

You can view my post about that with screenshots showing where and what to edit at http://materialboys.fr/2008/11/pref-setter-au-secours-de-dockspaces/

It's in French but screenshots explain it well enought.

I solved my problem this way. Hope it will help someone around there.  
(Version 2.10)