1. The way the Merge tables work occasionally lead to that message appearing when your table isn't in grid mode. As long as you know you can't use grid mode (with PT4) then you can click the "do not show this again" option on the message box next time you see it and things should work fine.
Setting the table skin to default should help avoid that message - using different skins or custom colours seems to affect the way the tables are detected somewhat.
2. If you see this again please take a screenshot
and attach it to a Support ticket
along with the PokerTracker4.log file from C:\Users\yourname\AppData\Local\PokerTracker 4\ (which you can access from the PT4 File menu) and the hand history file for the tournament.
3. I'll check into this and number 2 myself as well, thanks.