I'm afraid that I'm not going to update the "old" GrogBot anymore unless there's something terribly wrong. For a workaround to the team joining prob, you could set the corresponding team limiting cvar to 0. For example, in helms_deep, you could write "mp_pirates 0" (without the quotes) in the console to restrict the bots joining pirates.
The waypoints are poor, I know, as they were made in a matter of minutes. Still, the wp bug in desertruin you told about was supposed to be fixed in 1.1. Seems like I somehow managed to include the wrong wp file again >
(You're using 1.1, right?)