Through some testing I figured out the following:
Whenever I select a waypoint to go direct to, the FMS instead selects a waypoint 25 positions further down the flightplan list of waypoints. consistently, regardless of waypoint selected.
This would explain why in my previous flights it would just "delete the flightplan" as I was trying to proceed to a waypoint on the arrival, and there were less than 25 waypoints left on the flightplan, so it would just proceed directly towards the end.
Demonstrated in the following unlisted Video