Date Modified on folders changes globally after crashed

Our server running Windows Server 2003 R2 shut down unexpectedly due to a power issue and the battery back didn't kick on (a separate issue). After starting back up, all of the folders on the server have updated their Date Modified to the current date. This
wouldn't be a problem except that my differential backup see all of the folders as modified and backs up everything during the differential backup which doesn't work for me. Is there a way to revert this change or prevent it in the future?
EDIT: Also, The C: drive is not affected in this manner - only the drive that stores our job data.

Hi,
Based on my research, the Date Modified changed could be due to corrupt Update Sequence Number Journal. The USN Journal is a feature of NTFS which maintains a record of changes made to the volume. 
You could try to refer to article below to check if it could resolve the issue.
Error messages when you try to gain access to an NTFS volume
http://support.microsoft.com/kb/311724
Best Regards,
Mandy
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