Code red. Classic mono to poly mistake: trying to make the two romantic relationships into one big one. Your girlfriend needs to learn this right now. The two relationships are different, and each has a sub-relationship that Cindie listed. They will grow at different rates, and if the lines start blurring, problems will happen. Needs might get ignored, and someone might get displaced. Speaking from experience here.
How much time did they spend talking about opening up their relationship before they did? Did you and him talk before you and her became a couple? Do you know if he had any reservations, or if she just kind of pushed him to accept it? You mentioned that the first few talks were weird. Rightfully, so.
Your girlfriend needs to be a bit more considerate. Did she actually ask her boyfriend if he minded if you were there on one of "their" days, or was it just assumed because SHE wanted you both around? Togetherness is nice, but you need one-on-one time with her. He needs one-on-one time with her. There is no rule that says the three of you have to be together. You can be cordial and friendly with each other and do things together from time to time.
If she cannot be herself around you, who is she when she is in your presence? Why is that comfort missing? I hope she gave a reason or something for you to work with.