Re-imaging was successful, but nothing changed? Can try NI MAX to reformat. Similar procedure, but just right click on CRio in MAX for options.
http://digital.ni.com/public.nsf/all...257051006573CA
A couple years ago, I had to telnet in a delete the FRC files due to corruption, but the CRio was having more issue then you are having. It's a UNIX like OS on the CRio - VXWorks - Telnet, FTP, and you can even point your web browser at it.