The only thing unique abut the master is that when the system is in sequential mode (the default) it is allowed to run at the same time as another zone. You might try setting the system to concurrent mode:
Options page > Station Handling, uncheck Sequential and save changes.
Then go to manual mode, turn on two zones at the same time and check the voltage on both. That may give a clue about what’s going on.
FYI
I am planning to release a major software upgrade later today.
Dan