As you say, you shouldn't be made to feel akward in your own home.
Obviously when someone new comes along it inevitably carries with it a change in routine which everyone needs to adapt to, but it sounds like this is a little bit beyond that.
Broach the subject with your friend in a non-agressive way and see what he has to say about it. If his boyfriend is ignoring you and spending all the time in his room your friend will be unable to deny that it's causing a rift between you all. What, if anything, gets done about it is a matter for the discussion.
Perhaps you can get him to agree to spend more time with you guys, or maybe you can get him to invite his boyfriend along to your nights out. That may be the compromise you need to come to. Whilst I don't agree that a boy/girlfriend should be given priority in all cases, you will need to accept that in a lot of cases he's going to spend time with him. The trick is obviously to strike a balance.
The major issue in your case is that the problem doesn't lie with your friend, it's his boyfriend, so be careful not to put your friend in too much of a difficult situation. All you can really do is put it out there that things are not well in the house and that you have suggestions x, y and z to help fix it. If he chooses not to listen or chooses to bury his head in the sand there isn't much you can do.
Clearly his boyfriend is forcing him into a difficult corner over it and he needs to be strong enough to say no.
Christmas to a child is the first terrible proof that to travel hopefully is better than to arrive - The fabulous Mr Stephen Fry.