What the readers say
Give the guy a break -- he only signed a lease with his mate three months ago and probably wanted to turn the apartment into a bach-elor pad. Then you and his own girlfriend came along, and now he's having to adjust to having girlie stuff and someone else's relationship in his face. Give him his space and he'll come around eventually.
Listen to your boyfriend: he's the one who has to live with this guy all the time, so the flatmate would surely have said something to him if there was a problem. Maybe he's just keeping his distance to let you guys have some privacy and to keep some for him and his girlfriend. Either way, provided you aren't taking over the flat when you're there, it's not worth worrying about.
Your boyfriend needs to start standing up for you. This flatmate clearly has issues in his own relationship and is jealous of yours. Get your fella to talk to him, to explain that he pays half the rent and has a right to bring his girlfriend back without being greeted by a frosty atmosphere.