I think the difference is in the layouts of the theatre. in most broadway theatres, such as phantom's theatre, all audience members face the same way, and half the fun of doing the wave is doing it in an arena type setting, which the circle in the square is. there would be no point in doing the wave in other theatres, becuase 1. it would last 3 seconds a pop, and 2. you wouldn't be able to see anyone else doing it.
since the circle in the square theater is designed like an arena, and may remind some less savvy theatre-goers unlike yourself of a concert or a baseball game, it's just innocent fun, but it's understandable fun.
did it ruin the experience of the show for you? becuase it shouldn't have, but from your thread, it sounds as if they ruined your entire night.
"I'm an American, Damnit!!! And if it's three things I don't believe in, it's quitting and math."