I have a Mark V head and a helix and I actually can't get the ext-amp switching to work. I'm using a Hosa STP203.
If I pull the TRS end out of the helix slightly, it will change the channels. This is likely due to the tip/ring shorting to ground as it gets pulled out.
What cable are you using with yours? I can't find any information about what is happening internally in the helix when you toggle the ext-amp control on a patch/snapshot after assigning the switch in command center.