Reply to "MTH remote control box, in line with Z1000 transformer doesn't work. I wonder why?"

It could be the switch. If you can remove it and make the same contacts wire to wire, in both configurations and it works, then the contacts in that switch are incompatible.  Usually it is point materials.   (Ive run into this with points blocking serial data after I replaced the relay with the "alternate". )

Another switch type or brand with brass to brass contacts should solve it if it IS a toggle internal contact point issue.

Also, every one in a whíle the pins of a switch are not in a normal arrangement. They do this to please big buyers at times.

There are usually numbers &/or letters next to each terminal that will match a tech sheet on the switch. Ideally you check with a meter, but expect to follow any numbers vs a diagram or map position.  Likely doesn't apply... just one of those "sometimes" notes.