When using [timer:x] on a sign attached to a gate. (in this case, it's directly on the gate), the gate opens, then closes immediately. Then, after the timer expires, it opens. Clicking the gate a second time, causes it to close, then open immediately. Then, after the timer expires, it closes.

I believe the immediate reaction is the issue here. Without it, the timer would seem to be functioning. But the immediate "undoing" of whatever action was executed, causes the timer to do the opposite of what would be expected.