I'm concerned about "lost session config". Everything was supposed to upgrade smoothly, in fact there aren't really any changes to the the way sessions are stored, so as long as you installed over the top of your previous build everything should have been there.
If you installed into a new location so you could keep both versions accessible, then yes, any sessions you created in the old version would not be visible to the new one. This is the main reason I added the User File Folder, to get sessions and scripts out of the installation directory and into a place you control and can be shared by multiple installations if necessary. If you do have two installations, then you can copy files from the old installation to the new one, but I'll have to make a list of exactly which those are.
"but it starts playing immediately after I load the MIDI file instead of waiting for the track to start"
So you have an audio track recorded and running, and a MIDI track set up to follow the audio track.
Then you use Drag-and-Drop or "Load Loop" from the menu to load something into the MIDI track?
This might have something to do with the new parameters I added for snapshots. Internally all file loading behaves like a snapshot restore, it's just that the snapshot only contains one loop. In the Session Editor click the Globals tab
and the General category. The first parameter should be Snapshot Restore Mode. Set that to Stop if it isn't already.
If that doesn't fix it, then it's something else. If that does fix it then it raises some questions about how things
should behave when you do individual loop loading vs. restoring a full snapshot. We may need two different parameters, or just make the rule that individual loop file loading will always leave the loop stopped.