I also had problems with the initial setup after upgrading. Under Preferences-File, I checked 'reload most recent file' but PT never did. Then I noticed something strange- when clicking on File, at the bottom where the 5 most recent files are listed, the $Options.seq file would appear. I realize it's an seq file, but PT obviously can't play it.
Only after the $Options.seq file was demoted did it display my desired preferences. Hope this makes some sense. Beats me.

Additionally, the Looped Playback feature is acting up since the upgrade. Some files are not looping at all, and others incorrectly. Once again, beats me.

PT was the most reliable workhorse. Don't know what happened.

Percy