The likely cause of this issue is an NTFS USN Journal wrap. Please try increasing the size of your usn journal to see if your problem goes away. The following instructions will increase your USN Journal size from the default of 32MB to 128MB. If the journal is still wrapping you can increase the size even further.
From an elevated command prompt:
fsutil usn createjournal m=0x8000000 a=0x2000000 c: