Hey, I'm having the similar problem. It always chooses they/them, no matter what I choose. Do you mind sharing how you fixed it?
Viewing post in Pronoun Tool for Ren'Py comments
Oh my, it was a couple of months ago... I think I was lacking code that would actually call the pronouns. I think I was missing these -- after the custom buttons I made... I think.
$ selectedpronouns = pronounlist[pronoun]
$ they = theylist[pronoun]
$ them = themlist[pronoun]
$ their = theirlist[pronoun]
$ theirs = theirslist[pronoun]
$ s = slist[pronoun]
$ es = eslist[pronoun]
$ are = arelist[pronoun]
Or something like that. Sorry I cannot be more specific, I am still learning...