Hi there—thanks again for flagging tracking issues affecting the Commuter Rail.
The existing tracking technology requires a member of the onboard crew to access a panel in the train's control car and input every trip assignment, much as you suggested. The reliability of the existing hardware, coupled with occasional operational constraints, will at times result in trains not being tracked in real time.
As was noted, a program is underway to replace the AVL tracking system for the Commuter Rail fleet. The new hardware will be more resilient, and the system will operate in a more automated way not requiring an onboard input for every trip; this all will drastically decrease the number of trips that go untracked and the associated customer frustration. That new vehicle-tracking equipment is currently in its testing phase, with a full rollout expected this calendar year, however at this time a more precise timetable is not available.