We were able to lock the Y-arm using Megatron and the RCG generated code, with nothing connected to c1iscey.
All relevant cables were disconnected from c1iscey and plugged into the approriate I/O ports, including the digital output. Turns out the logic for the digital output is opposite what I expected and added XOR bitwise operators in the tst.mdl model just before it went out to DO board. Once that was added, the Y arm locked within 10 seconds or so. (Compared to the previous 30 minutes trying to figure out why it wouldn't lock).