L.,
While I haven't experienced exactly your scenario, I have had a reflux baby... and as much as I love my son... seriously, my heart swells with love for him, he was a very challenging baby and I can relate to the stress of this like you wouldn't believe. Even now he is high maintenance, and whiny and cries more than I would like... ugh! But when he's happy, he is SUCH a lovey boy. :)
So on to the lack of relations between your two. Perhaps your son just hasn't enjoyed having a baby sister yet. Honestly...maybe her crying scares him, or stresses him out. In which case, I think that instead of trying to comfort her or deal with the crying, he simply ignores it.
I am willing to bet that once your daughter is a bit older, has outgrown her reflux and becomes a bit more interactive he will find pleasure in having a baby sister.
I second some of the other suggestions... in the respect that maybe the grass isn't greener on the other side :) I would be wholly grateful if my son would show a bit less interest in his baby sister... he LOVES peek-a-boo, and he uses his burp cloths for this game... he drapes his 4 mo old baby sisters whole face with a burp cloth, but i think because he's waiting for her to say 'where's baby' he fails to take it off so she sits there with a cloth on her face while he walks away with his arms held out saying 'where is she?!?' So we have to keep a really close eye on him to make sure he isn't suffocating his sister :)
It'll come... :)