Known issue, when a train's schedule changes the station tries to recompute the signals, but when the train switches surface with the space elevator the train station can no longer see it in it's incoming list.

I'll have to partially rewrite the mod for that and i simply don't have the time or will for it right now.

Also the damage is minimal, the only time you really "need" the signals for circuit purposes is during a pickup so you know what to buffer, and a train is always picked from the surface of the supplying station, its only when a train changes surface to make a delivery that it loses the signal as it reaches the delivery surface, and i have not yet found a use/need for a receiving station to know which deliveries are inbound in regards to unloading capacity.