After I run CCleaner 3.08.1475 (64 bit) on Win7 (64) Microsoft Security Essentials says I may be unprotected and asks me to run a virus scan. I'm guessing CCleaner is wiping it's memory of it's last virus scan date. This just started happening within the last two updates.
This is caused by the MS Antimalware checkbox. All it does is remove logs, it does not hinder the performance of the program.