If you went from (32 bit) 8
.63 to 9
.9 there is a good possibility there were (intense) post-upgrade install tasks running.
There were file name corrections (happened due to a bug), sometimes upgrades perform DB structure changes.
I don't ever remember Calibre popping a 'Please wait (and don't kill this), while the DB upgrade completes' message. You went from 1 release level (8) to another (9), give it at least as long as a full 'Library check' takes before worrying