What's your regular routine when you start the game? Do you immediately grab the nearest planet to fly off to, or do you stop to look at the map? I've noticed just a tiny bit of wonkiness with the homeworld trigger. The random two items in my Drives'R'Us mod sometimes show up after a really short delay. It's less than two seconds, but it might help to wait just a heartbeat before leaving Glory.
That's not likely to be the problem, but it's easy to check and rule out. The rest of my ideas involve tweaking with the files to find a solution:
Do you have other quests with KEYS Zorg? If so, it's only going to generate one of them. You probably already knew that, or else you wouldn't have included that KEYS line. But, it's worth double-checking your files to make sure you don't have any other quests that might be triggering and preventing it due to the KEYS. Just to be safe.
Did you make similar quests for the other races? If so, check them to see if you accidentally left one of those quests with KEYS zorg as a copy-and-paste error. If there was a Muktian Quest that accidentally had Zorg KEYS, it could be causing the trouble without you knowing it.
Also, regardless of whether or not you have any other quests with that KEYS, you should make sure you don't have any other quests that modify the zorg behavior. If you do, deactivate all of them, and launch the game again. It may be that some other quest is triggering before or after this one, and is muddling the results. I know, it's annoying, but it's the only way to be sure.
Are the other alliance-changing quests set to "FLAG always"? IIRC, when multiple quests have the same KEYS, and are set to FLAG always, the game doesn't randomize them, it just takes the first one on the "game.ini" list. I
think the only way to get random quests is via the "event" and "mainquest" FLAGs. You only get a certain number of events per game (2 to 4 by map size, if you don't go into "distribution.ini" and change it), so you'll need to be aware that having these alliance-changing quests may reduce the number of events.
If those tests and alterations don't fix the problem, you might try changing "endquest" to "break", and at the start of each game leave Glory and then immediately return before setting out a second time. I don't think it'll come to that, though, as I suspect the problem involves the KEYS, or some similar quest duplication / overlap problem.