Just checked this again today, there were too many reports of issues like this recently for the (very rare) bug I had in mind when I answered above, so I thought it might be worth a closer look.
Turns out that currently some parts of profiles that I added recently aren’t handled at all when updating the database, i.e. not all settings in a profile are transferred correctly during the process. Will fix that for the next release.
Unless you actually encountered the odd bug I had mind originally, things should work again as intended beginning with the next update. Just in case it still makes sense to make a backup of important profiles as described above. That works correctly regadless of the database update issue.