File system issues on system partition

Hi all,

I have a Dell PE2800 sever running SBS 2003. I'm getting the following errors in NTBACKUP.

Error returned while creating the volume shadow copy:0x80042306

Warning: Unable to open "C:\" - skipped.
Reason: The volume does not contain a recognized file system.
Please make sure that all required file system drivers are loaded and that the volume is not corrupted.

In disk managment it shows the C drive as NTFS and Healthy (system).

The only releveant event log item is this
Event Type: Error
Event Source: VolSnap
Event Category: None
Event ID: 34
Date: Monday 02/11/2008
Time: 23:01:26 PM
User: N/A
Computer: server1
The shadow copies of volume C: were aborted because of a failure to ensure crash dump or hibernate consistency.

This all happened a month ago and when I rebooted the server then the system partition was so bad that Windows setup, reocvery console, etc would not recognize it as being there. Luckily I had just started using Symantec BESR (formerly Livestate) so I could take the last backup which is about 1-2 weeks old of the system parition and just put it back in place. This poses some issues with data on the data parition (D) like Exchange, SQL, etc because the system parition is from a week or 2 ago but the data is current.

Research so far shows a chkdsk or manually removing com+ (through recovery console) then reinstalling in windows maybe fix this issue. However, I would prefer to not reboot the server for fear of it's file system being unrecognized again and having to restore the parition from BESR image. Is there a (safe) way to fix this while staying in Windows?