I have two #6 DCC crossovers (one left, one right) on my layout which is essentially an inner loop and an outer loop connected by the crossovers. I use an E-Z Command Controller to run two trains and control the crossovers. When I power up the E-Z Command and test the crossovers they both work fine and will toggle back and forth.  The problem arises when I exit the turnout control mode and start operating the trains.  When I go back into turnout mode, only one of the crossovers responds. The other one (the right one if it helps or matters) does not respond. The only fix I've figured out is to press the stop button to bring everything to a halt and then press it again to start everything back up. That seems to reset things because when I go back into the turnout control mode both crossovers will work again. However once I exit turnout mode and then reenter it the right crossover stops working again.  I'm at a loss. Could I be temporarily shorting out the crossover? It initially works so I don't think it's defective but then again I really don't know.
I'm a newbie so I apologize if this is very basic stuff but at the same time I kind of hope it is as hopefully that means it'll be a quick fix. I searched the forum to see if anyone has encountered this problem but didn't see a similar post.
Thanks in advance for your help.