It actually does do an automatic background scan of digital channels (Clear-QAM, and ATSC.) I haven't seen MC actually lose a Guide listing due to it; however, I have seen it frell up (sometimes so seriously, that I had to re-run TV Setup to fix it) my QAM channel mappings (thank you, BHN, for wonky PSIP data!) As such, I have that function disabled on both of my machines.
To disable the background channel scanner:
Open Regedit. Go to HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Media Center\Service\BackgroundScanner. You may or may not see a value there namedPeriodicScanEnabled (if it's not there, create it (as a DWORD value) in that folder), and set the ValueData to0. (for future reference: 0= disabled; 1= enabled.)
Close Regedit, and reboot.
Standard warning: incorrect editing of the Registry can have far-reaching (and sometimes catastrophic) consequences, and may require reinstalling Windows to correct. Proceed at your own risk!
Required warning on the BackgroundChannelScanner: you cannot run TV Setup (when you're using digital (Clear-QAM and/or ATSC) tuners with this service disabled. If it is disabled, TV Setup will fail (hard-lock) on the 'scan for additional channels you may receive' portion of setup. If you need to re-run TV Setup, you must first enable the service.
If this fixes your issue, great. If it doesn't, you can always re-enable the service (just set it to 1), and we can try something else.
HTH,
Chris
MS-MVP (Media Center) [If this post helps to resolve your issue, please click the "Mark as Answer" or "Helpful" button at the top of this message. By marking a post as Answered, or Helpful you help others find the answer faster.]