The only thing I'm having problems with due to all the recent updates is with split/sector times, although it's actually the same problem that was happening with any of the autocross layouts, so nothing new, just bit more pronounced.
Its just that with the new open configurations, you can have different layouts even with the same track x/y config names (e.g. AS21, AS22, AS23.... AS29), but lapper still sees them as AS2 and will overwrite people's PBs especially if one config is shorter than others (assuming they're faster).
This basically ruins the use of the !top command and your Pitboard, etc.
Could lapper be changed in anyway so that it would recognise more than just the normal track names (short and long)? Instead of just AS2 or AS2R, maybe AS2X_A22?
At the moment, I'm just backing up and removing my PBGrip database files and letting lapper make new database files for new open layouts.
Unfortunately, that does rely on me remembering to change the files as appropriate.