Okay, when you open that file scroll down until you see something like this. (Rogue starts are considered by the game as planets right? It's been a while sense I've played a mod with them)
The count that's probably causing you problems is the orbitBodyTypeCount. This is simply a count of all the orbitBodyType lines in a planetType section. So whenever a planetType mentions a rouge star, just delete that orbitBodyType line and then reduce the orbitBodyTypeCount for that planetType by one. If a planetType references only a rouge star and nothing else, it is probably okay to leave it (as that shouldn't be part of the map generator). However, if you choose to delete the entire planetType section you have to reduce the planetTypeCount by 1 as well.
Another cause of the problem could be related to the super pirate base, but I need to know if they have a seperate entity file for it or not.