Our DS is only 6 weeks, but I think he has reflux too, and he's mostly doing 45 minute naps during the day. I'm trying to pay more attention to what he's doing before, to see if it's too much activity and he's over stimulated. I know the BW books say the short naps can be either from being OT, or OS, so that may be something to consider. She also says that if he's eating small amounts, he may not have the energy needed for a full A, so maybe when you are putting him down, he's expended too much energy since he didn't eat that much at 7:30.
I'm new to the forum, but recently reread the BW books to refresh myself, and just from what I'm doing with my LO. Sometimes I notice that he'll sleep through, or at least will allow me to help him transition if he does wake up.
Good luck! We share your frustrations!