I asked one of the employees while I was waiting and she confirmed that the state will not let them run together, so for every zumanjaro cycle, there are two ka cycles. When I ride ka, I saw the process clearly. They ran two trains (at the time, at least) and loaded and dispatched both of them to the launch, about which time Zumanjaro finished its cycle. I noticed almost no delay of the dispatching of Zumanjaro, and Ka's was minimal. They are certainly making the best of a bad situation.
Also, I used the single rider line both times I rode Zumanjaro, but I think I actually would have been better off on standby. The single rider line is shorter, but only moves in increments of about 3-8 people, while standby is closer to 18 each cycle. If anybody uses the single rider line, I suggest watching the last person in the standby line, to see if they ride before you.