However nearly every time i do a boot scan a Win32 pup of some variety shows up.
avast PUP scan is default off exept for in boot scan ...... so if you want PUP detection, turn it on in all shields where you want it

Boot scan info http://www.avast.com/en-eu/faq.php?article=AVKB132#artTitle

Important: Please be advised, that the Boot-time scan is an advanced and purposeful feature designed to be used [b]only[/b] when there’s something bad going on the system, and usually takes some time before it finishes. That's why it cannot be scheduled to run every time the computer starts, but as needed only.