So now it's not possible to join custom games that others have setup.

This was the best I got, in all other available matches every join button was missing.

You could try hosting a game, and, if the host screen comes up ok, cancel your hosted game and then, without quitting the game, go back in to the game you're trying to join.

The problem is, this screen sometimes defaults to transparent controls for some reason: if you can get the screen to initialise properly, the non-transparent stuff will "stick".

I'm not really sure what you mean about tranparent screens? Are the buttons there, but not visable?

Why would the top join button load when the others didn't? Is it something to do with the setup being different for player 1?

I'll try that hosting solution next time it happens. In the past I've found that things can be made to work if you spectate a game (provided there's one to spectate) and the quit straight back out of it, or I'll do the same with a tutorial match. Hosting would probably be quicker.