So what's the point in disabling "junction derail" if its still gonna keep derailing??? I have this same issue with TSW 2020. Two editions further and you guys STILL didn't fix it... I bet that this option doesn't work either in TSW 4, lol. Hire yourself a good programmer that can fix this LOVE. You certainly have the money for it (considering how expensive the DLC's are). Or simply leave this option out of the list (since it doesn't work).
That specifically disable junction derailments, mainly due to overspeeding. However there are some routes, Cane Creek, where you will derail on manual points when they are set against the train direction, even though in reality they would just push over. There are also a few bugged timetable runs around where you will derail even when stationary, due to bounding box collisions.