It sounds to me like you had the sensing wires for the 1054 in the same conduit as the rest of the wires.
The input impedance for the 1054 must be pretty high, which means that it won't require much of anything to trigger a pulse.
I've seen this in industrial equipment, notably a gasoline fill station at the old Saturn plant that if the operator fell behind a ringer would go off. Since the electricians put the leads to the pulser in the same conduit as the ringer, when the ringer would go off the display showing how many gallons of gas that had been put into the tank would look like someone had hit the jackpot.
Based on the one diagram that I saw, I would tie the 5 volts to the "+"terminal on the 1054 board, and place a 1 watt, 2.7k resistor between "-" and ground. Now run the pair of wires out to a dry set of contacts on your gate controller. Dry meaning no power provided by the gate controller. Just a simple N.O. or N.C. contacts (N.O. preferred).
Do your own math to figure out the resistor size and power rating, it's not my best subject.
With the contact open, the resistor will keep your "-" at ground while your "+" will be held to 5 volts giving the maximum differential. Once the contact closes, the "-" will be pulled up to 5 volts, and will be the same voltage as your "+" input.
Now if there ever was an application screaming for isolation, it's this one. One good lightning strike and you will not only fry your controller, but your home automation equipment as well. This is a common problem with copper phone wires where they work fine in dry weather, but become scratchy when it's wet. The reason for this is because the insulation is riddled with holes from lightning strikes.
I would wire up the inputs to opto-isolators and place that board in a weatherproof box and mount it outside the house. Be sure to provide a ground to give a strike a better place to go. That would require some new hardware at the gate end of things to drive the input side of the opto-isolator.
At the very least, use a USB isolator.