I'm not sure if the dark blue gates are controlled by the dark blue squares. Some of the colours match, some don't. They are all controlled, however, by the squares opposite them. For instance, the gates at the top on the left wall are controlled by the squares at the top on the right side of the board, and the gates at the left on the bottom wall are controlled by the squares at the left on the top side of the board, and so on.
Also, some of the coloured squares don't control gates but are timers for conveyors so that you can get out of jail, or off the train if you get on the wrong one, etc.
I'm not even sure if they are all timer switches, some may be round ones that you have to keep standing on.
If you press one and then have a quick look round with the shift key, you should see what it is controlling.
Watch out for the electric company, it's a doozy.
