There's a set of lights in the lower left-hand edge and on the very upper right-hand edge. When it's time to select a mission look for the yellow arrow near those lights. Hitting the lights lets you select a mission. Sending the ball up the ramp confirms the mission. I don't quite remember what the missions were - typically "hit some combination of things" - but they were worth a lot of extra points and/or an extra ball.
IIRC, it was a decision based around not porting to 64bit in the newer versions of Windows. I agree it's a shame it didn't move forward... same for a lot of things that were in earlier versions that didn't make the cut.
Man, Gamefaqs always had such amazing guides. I always wondered how these people knew every single little thing in the games they wrote walkthroughs for.