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I think that you do have to un-inhibit the modules in the I/O tree before you attempt to schedule the network.
When you schedule a ControlNet network, RSNetworx for ControlNet software interrogates all the connection originators so that it knows how to create the network schedule.
If your connections are inhibited, RSNetworx will probably not place them into the schedule because they won't show up as connection requests from the connection originator (i.e. the ControlLogix).
I can't be absolutely certain about that answer; I've never tried to schedule inhibited connections.