Thanks. I ran it twice, but forgot to reboot in between and running it a third time after rebooting caused more of the updates to take effect.
With the latest version I am able to collect IQ data from all 4 channels (8 voltages) simultaneously. Note, the Oscilloscope GUI did not update (it still places all 8 voltages under cf-ad9361-A in the oscilloscope device list, even though only 4 come from a single chip). Despite this, however, I am able to set independent LO frequencies in the "AD9361 Receive Chain" section of the control tool for both the ad9361-phy and the ad9361-phy-B, and verify that the separate AD9361 chips tune to the correct frequencies.
Thanks for the help