I have a 3 year old son that recently started having issues with my girlfriend. A little background about our situation: I got divorced from his mom about 1 1/2 years ago. Our son was 2 then. He is now 3. He lives primarily with his mother. I get him every other weekend, a full day during each week, and 5 days during the week every 6 weeks. I have been seeing my girlfriend for about a year now. He has known her about that time as well. She has a daughter that is about a year younger than he is (2 at this time). Our relationship is going well and is serious now. Until recently she and my son got along just fine. About a month ago he began crying randomly for no reason when she is around. He huddles around me and will not leave my side to go play or anything. If I go downstairs to the basement to do laundry, he cries even though he knows where I am at. He hardly plays with her daughter anymore. Like I said, everything seemed great up until about a month ago. He used to play with her daughter, he used to communicate with my girlfriend and everything else. My girlfriend treats him great. She has never done anything to him to ruin his trust. She does not yell at him or hit him or anything like that. She will correct him and make him sit in time out if she sees him do something wrong and I am out of the room. But, this has occurred nearly the whole time they have had a relationship together. Even when all of us are in the living room together, he just kinda sits there. He will not play or interact with anyone. He wants to sit as close to me as possible.
A few things come to mind. The first is separation anxiety. I believe he is afraid of me leaving him or has a fear that she is replacing his mother. Maybe he feels like I abandoned him when his mother and I split up and when I leave the room he is losing me again.
Second, I have a fear that his mother is saying negative things to him about my girlfriend and I. I have really no way to prove this or really anyway to stop it if this is happening.
It mainly bothers me that the problem has suddenly appeared. It would seem different if it had been like this for the last year but all of a sudden starting I am at a loss.

My questions to anyone are: One what would cause this? Are my theories right? Second and most important, how do I improve their relationship? I am not the kind of man that can have a relationship with another woman and have issues with kids be it me with hers or her with mine. She feels like she is doing something wrong. I tell her she is not to reassure her and honestly don't know what else she could do. I appreciate any feedback anyone could give or any similar experiences. Thank you.