Actually, that might be a glitch again, but there are other indicators. The general fog should start clearing up, and the blooms on the trees start to get bigger and bigger. If those things are not happening at all, then it's glitched.
If they ARE happening, then you just need a few more aether loads. Even when you fill the Town Square engine, it may not open the Junkyard fog gate immediately if you run directly there. Head over to Smuggler's Cove to collect the sea flowers, which should be open, and when you get back the Junkyard should be open...for about 5 minutes. (It also closes again way too fast now.)
Regarding time and number of loads, @Jayhawk_Greencape is right. If that is all that I'm doing (one load after another), it usually takes 7-8 loads before the junkyard is open. I usually can't get enough with just one character, using my process of just "free" aether (not expending items), so I have to use a second character to get the junkyard open, then switch back to my first character to get the sea flowers and jump into the junkyard. And that is with almost no fighting and just running around collecting aether. If I'm doing other things and just go to Town Square when my aether is full, it can take 9-12 loads depending on the timing. It's really difficult with the few number of players active these days.
