This is a strange one (I have to imagine).
So I built this midi from the C3 template. The song has Pro Keys (and all difficulties/reductions). It also has three harmony parts.
Everything seems to look good in the original midi file itself: track titles were checked and OK.
But both the C3 Midi cleaner and Magma see the PART REAL_KEYS_X as a second HARM2 track.
(1) if I export midi from Reaper and put it straight into Magma, it apparently sees the Lane Shift instructions in the Pro Keys Expert track as an attempt to set a tonic note for HARM2 and "fails".
(2) if I use the Midi Cleaner first, the cleaner removes the lane shift instructions (saying that they are attempts to set a tonic note for HARM2) and removes them. If I then run Magma, it fails saying there are multiple tracks named HARM2.
As noted, in the "uncleaned" midi, everything looks fine (track names, etc). In the "cleaned" midi, it renames the Pro Keys expert part as a second HARM2 part and the content of the track are a COMBINATION of the Pro Keys part and the HARM2 part.
UPDATE: ok I'm a moron, as I somehow apparently copied the HARM2 take and it ended up being also on the same track as the Pro Keys Expert part (no idea how I did that), visually hidden by the Pro Keys part. Sigh. I'd delete this post if I could, but I guess it could stand as a "MAKE SURE YOU CHECK EVERYTHING BEFORE POSTING" warning to people...