If you have cleric and inquisitor class levels, and you select a domain as an inquisitor, then the domain must be the same as one of the cleric domains (see reference at https://www.d20pfsrd.com/classes/base-classes/inquisitor ). PCGen actively prevents selection of the Cleric domains for the Inquisitor Domain class feature.
Well, I see what’s going on, but man, fixing it is not a simple thing. The code that is blocking you is there to prevent domain overlap from the Subdomains.
Sorry to find the difficult ones. It was affecting my Dhampir Cleric/Inquisitor of Pharasma. Easy enough to work at low level, since there are only a couple of domain powers to keep track of.
I can convert primary domains easily. You mess with subdomains and that’s going to add several hours to this.