Usually the imported MIDI plays as 16 channel from the Melody track. Mute it? Set it to single channel?
Has it to do with this darn plugin maybe?

I always have problems with erasing an RT especially, maybe there's a hidden (performance) track playing your MIDI as generated audio.

What i normally do is make a copy of it to the Soloist track, mute the other, and if i am after the melody mute not wanted channels and delete all that's not needed.
As such i can always revert to the imported stuff on the melody track then when things go wrong.