Vista Tutorial - System file corruption

I am using some imaging software (Acronis True Image) which from time to time finds itself unable to read the opening sectors of both of my external USB drives, declaring them to be unpartitioned (not true) and containing no recognizable file system (not true--NTFS). Both drives check out fine with CHKDSK and Disk Management confirms they are healthy. I can recover from this problem by using the system file checker and rebooting, following which True Image can again read the disks correctly, but not for long, because the problem is back again within a day or so. Acronis Support is pretty clueless on this.
The reason I'm bringing this up in this forum is that I assume what sfc /scannow is doing is replacing some system file which is corrupt. Is there any way I can find out which file it is and why it keeps getting corrupted? There must be a conflict somewhere but I have no idea what it is, so any general ideas would be a help.

SFC operations are logged here: %windir%\logs\cbs\cbs.log

Are you quite sure it's not just the reboot that's temporarily "fixing" Acronis? In other words, if you reboot without running SFC first, does that help?