The boot-time scan has better detection than the regular scans because it allows you to scan your computer for infections before the operating system has started and before a virus can be activated
That was my main concern: The case where my pc is infected by a virus which avast cannot detect and this virus doesn't allow avast to scan files properly. Ok that could explain the fact that boot time scan detect the not dangerous PUP threat while regular scan couldn't, but that's not likely the case because my pc works as normal as always. I can think of only 2 alternatives:
a. for some reason boot time scan has a different behavior compare to regular scan (if so, why?), or
b. in scanning procedure avast uses some cache and because my first regular scan of the file was clean (since i had PUP scan unchecked) it didn't rescan it even though i changed scanning options (if that's the case i guess that's a bug)