EdwardSkira, I don't recall a movie theatre at MadisonCentre,... but I'm not surprise there was one before since they have a performing arts theatre in the lower concourse area. Likely killed by the double-whammy of Cineplex Grande opening at SheppardCentre around 1999 and new EmpressWalk in 2000 with FamousPlayer (then Empire and now Cineplex).
Steveve, I understand what you mean about the odd layout of the Cineplex Grande movie theatre at SheppardCentre,... but you have to remember SheppardCentre was built in the mid-1970s,... and the movie theatre wasn't added until 1998,... replacing a rooftop courtyard,... the movie theatre was just placed onto the mall roof and shoe-horned around the office towers.
Here's an image of what SheppardCentre looked like before the demolition-renovation,.... basically the same from about 1999 to 2016 Spring,... can you see the Transformer???? The Transform right there, resting on top of the mall,.... disguised as a movie theatre!!!!
Here's an image of what SheppardCentre looked like around 1990,.... basically the same from 1976 (opening) to 1998,... back then walking along Yonge Street and seeing trees on top of buildings was like - Huh??? Remember NationalGym and BlockBusters?
Here's what the above area looks like 2 years ago via GoogleEarth 3D,....