puxflux
2
Is this happening in a blank kit or one of the presets? In any case, press func+transpose to make sure that there is not a scale set for the problem tracks.
This is the only thing that I can think of off the top off my head, but even if there is a key/scale set for the track, the notes should be transposed while you are playing as well as recording. Are you playing the notes in with the trig buttons or an external device?