Just a follow up, I was in the car today trying to sort my creaking driver's air vent, so decided to take off the door card and have a look. No dice I'm afraid - was really hoping I'd find one of those adjustment locknuts loose, but they all feel tight to me. Didn't want to touch the actual adjustment in case I screwed something up, so I chickened out and put it all back together. If someone's braver than me, perhaps they can take a closer look, but for now, I still have a clicking window.
It's annoying because I worry that if something mechanical is loose, it's eventually going to break under strain. But I have absolutely no faith in taking it to a dealer. I'm sure they'd keep the car for a day or two then just shrug and give it back to me.