If you try to MIDI Record into a Divisi staff, you must go into Note Entry before pressing Record. If you just select a rest/note and press Record, then the new notes go into the Top divisi Staff, regardless of which stave you selected, over-writing what was there before.
I presume this is because all Divisi staves are on the same channel but display as different coloured voices, so the procedure is the same as for voices within one stave.