I tried the exclusions and the two shields that allow process exclusions (web shield and behavior shield) have no affect. After a bit more checking it appears to be the file system shield that is scanning and I can only exclude folders not a process.
That is correct, exclusions are not appropriate for this as the exclusion is on the file and not its actions, e.g. opening other files to scan them will in some cases cause avast to intercept that and scan the file. There is no exclude process function in the file system shield.
That said, I have in the past kicked off an mbam scan and actually watched the file shield activity and it didn't interfere that much, have you changed the default settings of the file system shield ?
I'm also finding that the current 1.6 version of MBAM is a pain in the rear as it has some serious spikes in CPU activity and that isn't down to avast it is all on mbamservice.exe in the XP Task Manager.
What mbam version do do you have and what is the CPU activity for mbamservice.exe ?
May not be present in the mbam free version though.
Not sure if you can do scheduled scan in the mbam free version (?) if so try scheduling it for a time when you know you aren't going to be too active.
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I'm not sure how the exclusion of the avast folder in mbam would somehow stop the CPU activity of avastSvc.exe as that wouldn't stop it scanning files being opened by another application. A happy coincidence I feel, but fine so long as it continues.