Just for the sake of posterity (and I'm not suggesting this will work for everyone):
I never had the throne fall-out problem before, but I did have the left orbit issue. After spending 5 hours yesterday fixing everything and adding all my mods, I got the throne fall-out once the game was reassembled.
I tried the dead-drop C-shaped foam in the throne: The ball fell out.
I tried the rubber ring on the track to slow the ball down. Worked great until the ball knocked the ring further down the track, then got trapped in the rail and ended the game. Also, it looked like ass.
Just for shits and giggles, I figured that maybe if the habitrail leading to the throne had a little more play in it--and JUST a little, so the screws aren't screwed all the way tight--the slight movement might affect the ball just enough to slow it down and get it in the throne.
Perfect throne shots every time, and no extra crap in the game to get it done.
Like I said, it might not work for everyone, but it's worth a try if you're out of other ideas.