The jobs we have had this problem with have had discrete hall calls, though, not serial link. Also, I don't think the A car being on inspection affected the hall calls, it would only happen if the A car was the slave and the B car was the dispatcher. We only noticed it after emergency power testing when building normal power came back on and the dispatching was swapped.
I know that it is important that the 2 busses are in phase between the two cars- with the meter on AC Volts 2 to ST2 should have no potential between them. But you mentioned that this is the case already, and in the cases I have seen the 2 busses are in phase.
Everyone is so busy here that no one has had the time or patience to call MCE tech support and wait the two to four hours on hold with a meter and print at the ready in the machine room! But that is probably what needs to be done, and then hope you get someone who knows what they are doing.
Good luck, if you figure it out report back here please, if I do I will as well.
1) Will the Car B take car calls?
2) On Car B, in the Spare Outputs Menu Options, look for these inputs to be high:
ISRT, ISV, ISVF (Each of these represents an "in service and ready" state).
If these are not active, your car won't respond to dispatching.
If this is the case, it could be software. It can occur on either car, rendering the supposed "active" car to be really not active at all, but everything will look absolutely normal from first glances. The suggestion to call MCE is a good one.
With an original post of June 13, I wonder what the outcome was for the OP. Maybe he's still analyzing the problem, maybe he called MCE and got it remedied. We'll never know, unless of course he reports back.
What might the chances be now?
I know I know, there will be some who come here begging advice and do return with updates and resolution and that's great! But I get slightly miffed at those who do call for help, the members take the time to respond, and you never hear a word back.