The "Write Harmony to MIDI file" and "MIDI File Harmony on separate tracks" are checked.

The melody harmony comes out fine. If I do not assign a "thru harmony" at bar 1, but in proceeding bars, no soloist (thru) harmony is created.

However, if I assign a thru harmony at bar 1, that harmony is written throughout the whole song. The problem is, all the other thru harmony assignments are ignored.

So, for example, if I assign harmony #113 at bar 1, then that harmony is used instead of harmony #173 at bar 12, and harmony #243 at bar 32.