All right. There's three things that could be happening. One possibility, which seems to be unlikely due to what you're saying, is that there isn't enough Aether in the Great Engine an Old Town. The second one is that the glitch is causing you from entering you entirely.
The third option is the hidden telecog glitch. You can still teleport, but you won't see the orange circle. If you stand right next to the gate (where the orange cog usually is) it'll teleport you right into the Junkyard as you regularly would. Let me know if you have tried this already. If you haven't and it still doesn't work, we'll send this along to the tech team.