The link between the junctions does not work if one of the junction is locked by a train.
Imagine there is a crossover in main tracks between two turnouts: J1 and J2. The turnouts are linked using the junction link in synchronized mode (i.e. both turnouts are set to the same direction) and you issue driver command to diverge from the right to the left track. When train approaches turnout J1 and comes within turnout trigger radius (say, set to maximum distance of 500 meters) both junctions are set in the left direction. This is expected behavior. When end of the train passes turnout J1, the driver attempts to unlock the junction and set it to the right direction, but this attempts fails, because turnout J2 is locked and both turnouts are linked. When end of the train passes turnout J2, the driver unlocks it and junction link attempts to synchronize both turnouts. But because both turnouts are already set to left direction, the junction link does nothing. Turnouts J1 and J2 are in sync, but now they are set to diverged direction, which is not the default direction. If turnouts are protected by a signal, this signal is likely to display red and cause a signal before to display yellow. This will force the next train to drive at half speed, despite the train drives in forward direction and it should be able to maintain maximum speed permitted for the line.
I think the problem is that the junction link script does not look into the default (i.e. set in Surveyor) turnout setting when synchronizing linked junctions. A solution would be to use the method suggested by Scottbe8 above, but not to synchronize only to set both turnouts to their default setting. It would be really nice to implement such solution, as properly functioning junction link would add safety and efficiency to driving trains in AI mode. As it is now, it is more of a burden and I removed the junction link from all my routes.
