If the rear cylinders were leaking there would be fluid. Did you see any?
Sounds more like a bad MC. The front and rear systems are stacked, in series. If one seal fails the pedal will drop that distance until the second one catches. Your new MC might fix it.
Here's a drawing, they're all the same. The right seal contains the fluid, the other two create pressure. You can see how you can lose one but keep pressure on the other end.