We and ED-E completed "I Could Make You Care" including taking out the silly Brotherhood guys outside the bunker. In our conversation, I said the choice was up to her and she said she just had to stay with the Brotherhood. So I started to go and she followed right along. Then I tried saying "Our ways must part" and she said, "Fine, I'll just head back to the 188 Outpost". That's not staying with the Brotherhood. So I reloaded and off we went on our journeys.

I don't understand. I assumed she'd stay in the bunker with the Elder and so on. Does it always play out like this?

Yes, she's decided to stay as a member of the BoS, but is still happy to follow you around the Mojave.

That's great! She's saved my bacon a hundred times over. Thanks for the reply.

Next time, keep in mind that you're better off convincing her to leave. The battle takes place somewhere else, not at the bunker exit, and you end up with better loot.

There really is no convincing. She leaves if you tell her to, stays if you do not. No speech check or any dialogue option required other than selecting the dialogue.