This problem actually started in June of 09 and has finally been resolved as of July 2010. The problem was, once a file was checked in to the vault, we could not move any files to new project folders. After working with our Var and them with SolidWorks we got a work around that worked. This problem started in SW09 and was still a issue when we went to SW10. The work around we used to correct this problem is listed below.
NOTE!!! Make a backup of the metadata and all files in the vault. Make sure there is a method to restore the vault in case of catastopic failure.
1) Make sure all files are backed up including archives.
2) Stop Workgroup service.
3) Delete \vaultdata\data\cache.store file.
4) Delete all tree*.pdmw from under \vaultdata\projects (Dos command I used was del tree*.pdmw /s).
5) Delete \vaultdata\pdmrc\project.pdmw
6) Restart the vault service twice. (Wait for till the vault is done validating before stoppin and restarting) This may need to be done a third time. We found that if the service started only once not all the files were viewable.
Hopefully this can help someone if one is having this issue.