Background: Note stems
The direction of stems is governed by five things:
How notes are grouped under beams.
Any manual manipulation of beams.
The Flip Stems function.
How the note information is set for each note.
How the Polyphonic tab on the Staff page of the Score Settings dialog is set up (if you use polyphonic voices).
The order of this list corresponds to the priority of the settings. On conflict, the grouping under beams has the highest priority and the settings made on the Polyphonic tab the lowest.
If you have edited the stem length of a note and then flip it, the stem is reset to default length.
If you have activated the “Fixed Stems” option on the Staff page of the Score Settings dialog (Options tab), a lot of the automatic stem length settings are ignored. However, you can still edit the stem length and direction of individual notes.