It's that game. I've definitely heard of issues with inter-game compatibility, especially with the earlier games.

RB2, LegoRB, and Beatles RB all use essentially the same game engine, and are generally compatible with each other. RB3 is compatible with earlier instruments, but also introduces the "Pro" instruments (and a "Pro" mode) which isn't backwards compatible at all.

I'll also bring down my RB3 Pro Keyboard, which isn't compatible with RB2-based games.