When Withers spoke to you about a bosom companion, did you get a dialogue option referring to Astarion? Also, I have noticed that since patch 3 the option to choose the dialogue that implies you didn't pursue romance happens in act 3, even while you are actively in romance with that companion. At least this happened in my current playthrough. That might be the reason it did not go away after using it.
If Astarion mentions that you should still be able to have Raphael owe you, then the long rest scene should trigger regardless of deal. I'm surprised it doesn't, seems like oversight for sure.
