As mentioned in the server tutorial, every input needs to have a signal sent to it to work.
This is rather time demanding for massive wiring mechanics that use hundreds of gates.
My suggestion is creating a "start up" scan that scans the whole map for gates and by that activating them.
Another way to do this might be to add a 3rd signal type that does not follow wires and does not execute any gate mechanics. So a signal that works over an area and identifies every input. So instead of sending a 0 or a 1, you send an X signal or perhaps a 2.