I've seen it happen many times too, not very frequently but repeatedly - yes. It is not a bug, it's feature.
The technical reason is that FMS logic suggests a certain NAVAID based on the procedure activated in the system. If you keep the RADNAV pg empty, or erase (*) whatever you have there when the message comes up, you would be able to observe what the FMS believes is the appropriate tuning.
It cannot be scrutinized from over here, as we have no way of knowing what procedure, leg sequence and active waypoint you had going on at the moment. Even if we did, we would need to see the definition of the legs (**) from the database dump, which may or may not include a "reference navaid" - that's where the FMS gets ideas from.
* = SOP, common sense, and airmanship requirements permitting
** = the FM DB coding does actually not consist of connected waypoints (as we may percieve), but track-to-WPT segments which are mostly made invisible to the pilot.
http://galileo.cs.telespazio.it/medu...inator_1.0.pdf