Darren, you now have a mission to accomplish

[darren]

I just put out a new minor release that will hopefully take care of the server map config issue (among a few others I found.) The change was basically to use default_mp.cfg rather than server.cfg, since if default_mp.cfg doesn't exist it will use config values built into the .iwd's . I also made a couple of changes to the punkbuster handling which should make it work more reliably. Let me know if these helped with the problems you are seeing or made them worse. You can get the updated version now by doing a forced reinstall in the WHM->cPGS menu.

[islanding]

Then should the command line start be changed to default_mp.cfg as well?

[islanding]

I used the custom command line to fix & set the start correctly and it worked fine. Server started correctly!

[darren]

If you stop and then start it should use +exec default_mp.cfg rather than +exec server.cfg . If you hit the "restart" button it will reuse the +exec server.cfg , so you may want to try the stop/start instead next time rather than having to set a custom command line entirely for it.
Let me know if you run into other problems with it.