IF YOU HAVE THE DCS REMOTE: On the soft keys of the remote there is a “Pantograp menu.” (The “h” was left off because it would be too many characters.) You may have to scroll though the soft keys, or even hit “more” to find it.
On that menu you can control which pantographs are up or down, whether you have automatic operation (which is what you are looking for) or manual operation. I doubt this is your problem because you did the factory reset, but you might want to change the settings in that menu. You also might try to do the factory reset afterwards.
You also might want to turn the power off, and pull it off the track for several hours. I have quite a few MTH electrics, and sometimes the pantographs get VERY confused. A long power off wait has always solved the problem.
You should also be aware that most MTH electrics have a separate pantograph control board. And there are two varieties. You will have to do a product search.