Hmmmmm, assuming we're talking about a managed SEP12.1 client here, can you try out the below?
Open up the "Virus and Spyware Protection" policy assigned to your machine, and navigate to Administrator Defined Scans -> Advanced Tab, and near the bottom, change the "Scan Progress Option" to "Do not show scan progress".
Incidentally, the randomly timed nature of the scans, suggest these are Active Scans initiated when new definitions arrive. You can disable these scans from the same area (just above the "Scan Progress Options" in fact).
This'll be different for unmanaged machines though.