When did you update? that message should be fixed now on the update.
If you run the installer it will repair that.
2) Now every time I start TS, it seems to think that another instance of TS is running - when it does not seem to be the case
The check for another running instance is a 2 way conversation, the starting app asks if there are any TS's running out there, if it is saying there is, someone must have answered.
Check your task manager, it will likely show up as javaw.exe in processes. I'm betting you do have a hung instance of TunerStudio running. It may have hung do to the above message., Actually the above message may be getting caused by the hung instance. It can not update the files if they are locked by another running instance.
3) The help message on the Vbatt calibration page refers to kpa when it should be Volt. (Still not quite sure how this is meant to be done - I've always used an adjustable resistor to fix Vbatt calibration)