If GSX says a gate is taken, then it's taken, no questions about it, since GSX ask the sim about it.
If the sim says an AI is there, but you don't see it, then it's surely a problem of the AI traffic program you use. Perhaps the AI is invisible for some reason (wrong/missing/corrupted model), or the AI program has just destroyed it to keep the fps up.
The only thing sure, it's not a GSX problem. Of course, you can probably easily test this, by re-enabling the default AI and don't start UT Live. That way, you can verify GSX is correctly detecting AI at gates.