Perhaps you are inadvertently transposing the midi part - either in the track’s MIDI Modifiers in the Inspector or via the Info Line in the Project Window. I just checked and if you transpose playback in either of those places it doesn’t take the transposition into account when creating chords from the Key Editor.
Also the make cords function just ignores any notes if it can’t figure out what chord they are in. For example if you have a bar of F and then one of G, but your G chord is only a G & D notes omitting the 3rd. When you make chords from this it will show the F chord as covering both bars which would certainly clash when playing the chord and midi tracks at the same time.
Have you gone into the Key Ed and selected the group of notes that was analyzed to produce the chord in the Chord Track and compared what the inspector says the chord is to what is in the Chord Track?