Heh, yeah the anti-stuck mechanic was a pretty neat idea I had, I'm glad I implemented it since it really makes the game a lot more fun and a lot less annoying. Most people I showed it to said the same thing: that the dimensions needed to be more obvious. I've come up for a fix for that which is using a shader to highlight each layer, so hopefully that should fix the issue.
Don't worry about not being able to get through the 3 boxes, that part is incredibly difficult (balancing issue from my lastminute level designing), it's right at the end so you weren't really missing out on anything.