I wonder how you were able to run the Live Update and not have GSX Level 2. The Live Update should have said you MUST download the new GSX full installer, otherwise it wouldn't continue.
So, if you just followed what the installer said, and installed the updated full GSX installer (which contains GSX Level 2), it would update JFK 2 as well, and would work with no errors.
Since GSX and Level 2 are both free to use at every FSDT airport, the issue is entirely moot here.