Yes, the grounds of the two transformers and the track would also need to be connected, and the grounds of any DZ1002 switch controllers as well.
Others on this forum have urged concerns with transformer phasing. I tried reversing a transformer plug with several issues I had. It had no effect in my cases. I have not pursued it. My understanding is that phasing is vital when you use section control: different transformers controlling train power to different sections of track where a single engine can cross a block boundary between the two transformers and potentially get double normal voltage if the transformers are out of phase. Particularly dangerous to newer locomotives with circuit boards full of sensitive electronics. If I understand, you are using one ZW for track power: it can never be out of phase with itself, so no danger to locomotives crossing block boundaries controlled by two different knobs. Based on my understanding, your problem will be unaffected by whether the Z feeding accessories and ZW running trains are in or out of phase. Of course, no harm in phasing them.
You could also temporarily use one knob of your ZW to control the relay and switch machines of your crossover, taking phasing out of the picture, and see what happens.
Personally, I was "sure" something was wrong with the relay. Touching the green wire to accessory power repeatedly and hearing the audible clicks forced me to change my thinking and look into the lack of a true common ground for the whole railroad. I still don't understand why it works best using train power. Someone's probably going to tell me it's because my transformers are out of phase (but I was using the same transformer for both train and accessory power).
