What do Manual shuttle train modules do?

Trains with them don't react to shortcuts, don't open the station list.

The trains with manual a module cannot be called like the normal shuttle trains.
When you ride such a train then the station selection dialog is available as with normal shuttle trains.

The idea is to have special trains like builders or artillery trains. They are controllable like normal shuttle trains but they shall not respond to shuttle train calls.

It works fine for me.

That's really odd.
The same save that didn't open the station list on a FARL now opens it.

Could it be that the train is dual headed? You need to have a module on each end - it's a feature ;-)

My FARL is dual headed.
Usually my OCD compels me to keep grids identical, but it's possible I was lazy.

No problem. Glad that this was the issue :-)