Hmm... again, hard to figure for me, having no comparable system :?
From looking at the sources, the only possible loophole which I can see is the Windows API function SHGetFolderPath (and the conversion of the result). From this point, everything related to the pathname of default.workspace works on wxStrings, which shouldn't have that kind of problem.
Can you look in Code::Blocks' debug log? It should say something like "Saving workspace some/path/to/workspace" - does this show the wrong path there too?
Problem is identified, is the same issue as it was with configurations. The same applies to projects as well. Yiannis will work on it this afternoon, since he can test it on his system, too.