Hi Dan:
What you're doing in your timing room is very unorthodox and invites problems. You said your A system operator is in communication with the finish and you are operating B system and communicating with the start. You also said that you, as B system operator, are advising the starter when to send the next competitor.
The usual, and safe way to divide up the duties on electric timing is to have A system operator in communication with both start and finish. The A system operator needs to be advising the starter when to start the next racers AND needs to hear from the finish controller which competitor is crossing the finish line.
If your B system has an operator, he/she should be listening in on the same line as the operator of system A so he/she is also aware of what is happening at the start and finish. As noted by FKP, though, you need to remember that the B system only needs to record raw times of day without operator intervention. There really should be no need to connect the B system timer to a computer as well. Remember that you can't just substitute net time from B system for a missed net time on A system anyway. You need to do an Equivalent Electronic Time calculation if going to B system for a missing time. This means working from raw TOD records.
As Chase wrote, you really shouldn't be doing anything with your B system that would hold up a race!
Steve