I had something like this happen last night, but it wasn't an boot-up scan. I had previously backed-up the contents of an 8GB flash drive to my W7 PC (running Avast! free edition), and was trying to copy the backup to a new 16GB flash drive. The copy started out normally, estimating 16 minutes to copy, then 30, then 3 hours. The file it was trying to copy at the time was a moderately large PDF (10MB). I checked back after 15 minutes and my PC was still trying to copy the same file. I thought that the flash drive was defective, but I first tried copying only portions of the backup to the drive (which coincidently had no pdf files in it), and that went quickly. I tried copying another portion of the backup (this time containing pdfs) and I saw the copy slow down while copying a couple of pdfs and then speed up again copying other files.
Lastly I tried copying over the last folder in the backup - this one had the problem pdf from my initial copy attempt. The copy process once again seemed to stall on the same pdf. At this point I got suspicious and disabled the Avast! on-access scanning, and the copy completed normally.
I'm surprised that Avast! seems so capable at scanning zip files and installers, but bogs down on pdfs. I'm wondering now if there is anything wrong with my 8GB flash drive, or if it was just Avast! slowing down the copy process as I made the backup.