@ Lars-Erik
Your AV is going to be one of the last things to be shut down, as for the file system shield scanning more files than it should, that is impossible. Since it is an on-access scanner and file activity is going to be scanned.
So you have a program that is still active and the file system shield would scan that activity. Unfortunately there is no easy way to determine what that activity is. But shutting down the file shield and the problem doesn't happen doesn't mean that the problem is with the file system shield. Not to mention shutting down the file system shield whilst there is unknown activity going on is a security risk.