To expand on my observations (which are purely “seat of my pants”) is that the likelihood of mal-positioned notes increases when the BeatBuddy Manager (BBM) encounters Not supported notes in the MIDI file. The inverse is probably true too: the likelihood of mal-positioning decreases (but may not be entirely eliminated) when the BBM does not run into Not supported notes.
You reduce the risk of not having mal-positioned notes when the notes in your MIDI file match the notes that are in the kit you are using in the BBM. I hope this example illustrates the issue just a little better:
Screen shot 0 shows at least 2 MIDI notes that most kits will not support F1 (41) and B1 (47)
Screen shot 1 shows how the BBM MIDI Editor displays (as a result of using 41 and 47; see how 35 appears as 36 and 38 displays as 39?)
In screen shot 2, I applied the workaround, which was to Cancel the MIDI Editor and then re-opened. Now 35 and 38 show up where they belong but the Not supported notes are still displayed
In this last screen shot, I’ve gone back to my DAW and moved only the Not supported notes to fit the configuration of the kit (added 2 semitones to F1 and lowered B1 by two semitones). Usually on the first try—but not always—when opening the MIDI Editor with the corrected notes, it will display everything correctly.
This may have just restated the obvious for you, however, it may serve to help other users just dipping their toes into transcribing MIDI source files into useable beats or songs for the BeatBuddy (BB).
Also see How do I go about building my own beats from midi files online