Solution
NI has wanted to add the new Dynamic Averaging measurement mode for the 9361 to improve on the existing counter-measurement methods. It provides better usability and fixes some bugs/limitations of the previous modes.
Unfortunately, the DAQmx Create Virtual Channel(CI-Freq) VI defaults to low frequency with 1 counter as the measurement method and also has the default for measurement time & divisor which are not great defaults. So, the decision is to report an error for the measurement method and tell the user to select Dynamic Averaging instead.
Dynamic Averaging is a superset of the other measurement methods. From the 9361 datasheets, Dynamic Averaging supports setting measurement time/divisor as follows:
You can mimic the other counter modes like this: