Hey Pokeminer,
So in *theory* it should work with additional Pokemon etc, but I did not do a lot of testing with custom pokemon or heavily modified PBS (I think the pokemon.txt I was using went up through gen VI). There are probably going to be some issues I didn't run into.
I also haven't added very much error reporting for such situations right now, but if you run the program from the command line it will at least tell you the crash dump which would help me to find where the problem lies.
I believe the only PBS it tries to read upon opening right now are abilities.txt, types.txt, moves.txt, and pokemon.txt. So whatever it's angry about would be in one of those files, most likely.
If you want you can PM me and I can look at running it with your PBS to work on fixing it, or you can just send the error, whatever you prefer!
To run a .jar from the command line, you can use:
java -jar <jar-file-name>.jar
You will need the full path, e.g. 'C:\Users\Unbayleefable\Pokemon-Essentials\CartographerAlpha1.2.jar' or wherever yours is located.
Edit: The current version at the time of writing (1.2.4) is generally better about reading the PBS files without crashing/hanging/etc. Also as of version 1.2.1 onwards, errors and other information is now logged to a log.txt file in the CartographerOutput folder, so it is no longer necessary to run the program from the command line to get the error information.