Maybe its not the alleged mess hes worried about...?
well, maybe it's because of his parents or he's embarassed or something.
Maybe hes given one of the lodgers the impression that hes single and interested in them? He might well be bedding one of them ?
Maybe he just doesn't think it's the right area for you to go to, he wants things to be nice with you and it's probably not quiet or nice to hang out in. Considering he has no personal space there apart from his room, I don't think it's the worst thing although you could ask to just go round for a bit? Meet the others before going out somewhere, just sort of slowly get round to going there more often?
Maybe he's married and doesn't want you meeting his wife..
Then it sounds a bit dodgy, do you know any of the people he's lodging with? Also, how old are you both?
He's probably embarrassed about the state of the place
.... hey.. i just wanne say ... the most important thing to guy's is a bit of privacy ... so if u was to invade his flat, he would have nothing to himself... and who knows maybe someone else is involved in your little ''equation'' between u n ur bf
Don't suspect him of anything if it doesn't seem likely, as Doc(1/cosC) said, men do need their privacy, for it to be 2 years everything else must be going ok.
Is it an unusual for the lack of conversation? If he's acting suspicious now then I think it's time for the talk.
EDIT: Mind you, there might be some issues that he can't explain that don't relate to cheating on you, I can get jealous or paranoid about my boyfriend and he really hasn't done anything wrong, you need to talk to him again to sort it, just tell him to be honest.