I tried TMNT: TF on a local build of Festalon (another quite accurate player engine), and on my experimental NSF player which uses an actual NES for sound output, and they sound the same as AO 2.0b6 (other than slightly different frequency equalizations on each). Here is the sample from playing the NSF through my NES:
tmnt_tf_47.mp3 (320K)
This isn't definitive though, since it's not running the NSF code on the NES CPU (my devcart doesn't have enough RAM to hold the entire NSF), and I don't have the actual game.
So, it could be 1) an error on your part, 2) the players, or 3) a problem with the NSF rip (in order of likelihood).