If you are trying to run 5.66 latency with 2.33 latency on the same network, and it actually worked, you just got lucky. The Conductor will only deal with one latency at a time. (Makes sense, since two latencies would require two beat packets).
If you are using the same latency on a single network, and the question is solely about persistance, there is a "persistance" bit that must be turned on when using CobraNet discovery (make sure you are using the latest version from CobraNet.info) that should allow the CM-1 and the CM-2 to keep their settings after a power cycle. I'm surprised that the CAB 16d can even do the lower latency, it is not supposed to be able to do anything but 5.66.
2.9.11(1) for the CAB 4n with CM-1 and 2.9.11(2) for CAB 4n with CM-2 is the only firmware that currently works with the 4n's. 2.9.12 is the current firmware for the CM-1 in the NioNode.
One last item, the lower latencies of CobraNet can be VERY, VERY tricky. Be sure you really need the lower latency, and do good research, to make sure your project is a success.
Make it intuitive, never leave them guessing.