I would suggest (unless Kovid says otherwise) that any issues with the new PDF engine you put on the bug tracker, attaching the pdf for Kovid to take a look at. It sounds like the new PDF engine isn't being actively developed right now, but at least Kovid would be able to replicate the issue whenever he does next work on it.
As for running the scan in the background, that isn't going to happen anytime soon I'm afraid. The only background processing mechansim I have seen in Calibre is the "Jobs" stuff that gets used for when you convert books. However the risk with it (and possibly the same reason why stuff like download metadata doesn't run in the background) is that you have all the concurrency issues of two different things updating the same book record at the same time. I don't know if you have ever noticed but it is possible to lose your newly converted book from a job if you happen to be editing metadata for the same book at the same time the job completes.
Now maybe this is something Kovid plans to address in future, such as with some sort of optimistic or pessimistic locking mechanism which would prevent you editing the same book a job was running for. If he does, then I am sure I could look into revisiting it. Right now, I don't want to run the risk of any database corruption by a user being allowed to edit a book manually while the ISBN is being updated in the background.