As a work around I just added another station after the Space Elevator that the train always goes to. After the train goes through that the Train Control Signals mod works as expected. Would need a Work around station on both sides of the elevator if using the signals on both sides. I've got the depot and refueling in orbit so only need the work around after the upwards journey.
So my routing is Elevator -> "Work around station" -> Depot -> Refuel -> Drop off