The one thing I don’t like about the boot-time scan is the lack of an option to setup exclusions. Because of this lack the boot-time scan has a tendency to carp on the efforts of and waste time on malware already found and quarantined by other anti-virus/malware programs. Other than that I think Avast is the best anti-virus program and I recommend it to my customers on a regular basis.
Although you can’t select what to exclude, you can select what to include:
http://www.screencast-o-matic.com/screenshots/u/Lh/1399328076178-90153.png
There is usually more than one way to skin a cat… 
Because of this lack the boot-time scan has a tendency to carp on the efforts of and waste time on malware already found and quarantined by other anti-virus/malware programs.why dont you just empty the quarantine on those programs....
anyway, what programs are they?
The boot-time scan should honor the global exclusions set in the program (Settings / Antivirus / Exclusions / File paths). Doesn’t it?