I ran into this problem yesterday as well. To avoid all that booting into Safe Mode and rebooting back into Normal Mode you can do the following to save all the hassle:
Right click the CIS icon in the System Tray and disable all features (CAV, CFP, D+, SB).
Open the Task Manager and kill cmdagent.exe
Now, do your bases.cav swap.
Go to->Start->Run and type: net start cmdagent (this will restart cmdagent.exe).
Re-enable all the CIS features that you disabled in step 1.
I’ve attached a small .bat file to restart cmdagent.exe instead of doing step 4. If you want to use it, instead of doing step 4, just double click cmdagent.bat (it saves some time).
On my system, I placed cmdagent.bat in the CIS program folder and created a shortcut to it. I placed the shortcut in my CIS Start Menu folder (I just named it CIS Agent) so I can restart cmdagent.exe easier whenever I want.
The update fix worked for me. However, ever since fixing it I have trouble with cleaning temp files with programs like CCleaner or WinUtilities. They get stuck trying to clean CAV**.TMP files from C:\Windows\temp. The only way to get CCLeaner work as it should is to temporarily disable Comodo Antivirus until the cleaning is done. ???
Those are .tmp files locked by AV.
Once you’ve cleaned them and reboot and run no additional scans they should not turn up or stick around long, CIS should clean these out once scan is finished…