Build, please? I've had no such issues with a similar junction up through T:ANE. It appears the points are in fact flipping. Any other trackside devices in the same area?
Lot of facors at play here. The Train is stopped, what is on the other branches? Is train in AI mode? Does the train have a schedula or being manually driven, what kuid is the switch, etc
So move the train, move a signal, change the speed limit if in AI (this actually effects the physics). Albert Einstein said "Insanity is doing the same thing over and over again and expecting different results"
I have had this occur once or twice. The issue had something to do with how I had my signals setup and I ended up simplifying things a lot. I'm not sure if it's a script getting lost, or the AI playing Rock-paper-scissors really fast.
Just a thought, I seem to remember in the past having too long a distance between signals which caused the AI to stop, adding an invisible signal fixed it.