There is a bug in Anytune 3.6 which sometimes causes Anytune to skip to the next track instead of looping when the B slider is at the very end of the track. It does not happen with all tracks, but will consistently happen on a particular track. We are aware of this issue, and will resolve it as part of our next update.
Here is a workaround for the time being:
For the song you’re having trouble with, select the B <-> loop adjust button. Then tap the minus button on the slider to the right of the button. That will move the B position back from the end of the track by about 0.005 seconds. Depending upon your song, you may have to move it back a bit further.
ie: Use the controls in this picture, but select the B<-> button instead of the A<-> button, and hit the minus key to move the B slider ever so slightly back from the end of the song.