I don't have other reasons, and I'm not frequently rebuilding the database. I noticed it happened when I had to update from the beta version of the firmware to the final version and it happened again earlier when we had a random power flash off and on while I was playing and the system did a system check and rebuilt the database when powering on.
I have multiple folder setups and a good chunk of games installed -- its annoying to have to re-do all of that whenever a database rebuild is forced.