Oh is that the reason, why she was invisible (but still talked to) when I had her with me at the counting house recently?
I'm going to guess that it is. It happened to me too at that conversation where the game was treating Jaheira like she wasn't on the team - she didn't show up during the cut-scenes and she didn't call out the clerk being nervous or anything like that. It was as if she wasn't there.
Re-loading to before the start of the conversation, making Jaheira drop out of starry form and then talking to the clerk resulted in the conversation going about as expected, with Jaheira bypassing that first insight-check and doing most of the talking.
I'm also pretty sure that her lines during the conversation with Glitterbeard were missing as well, as I had forgotten to take her out of starry form again after the fight against the Bhaalists. I *think* she should have lines here, but those never came... plus I'm very sure she was again not shown as present during the shots that show the party.
Some of her lines you get from her after those conversations are also slightly different, I think, and probably the versions you would get from her if she truly hadn't been there for the encounters/conversations.
