Dang! This was an extremely clever concept and well-executed, especially with a time limit. I'm impressed that you had the time to create a color-blind mode. And the puzzles are well designed - simple enough to solve in a few tries, but complex enough - especially once multiple boxes are involved - to make you think.
I found a bug where (I think) I switched a conveyor at the same frame a box went over it, causing the box to freeze in place.