First let me say that I'm not very well versed in Photoshop at all..
But I have had a similar situation start happening - where panels would not remember their size or locations, or expanded/collapsed status.
IIRC, after I 'blew up' the preferences folder by renaming it, the problem went away. So you may want to try that. If that helps, you can then start copying over your needed preferences in a 1-by-1, 2-by-1, or (...) fashion. As I don't really use PS, I just left it at the reset and reordered a new workspace and manually changed some Edit->Preferences back.
You may want to even just start with renaming the Workspaces folders and "Workspace Prefs.psp" file.