I think its because the front starts off lower than the back, and so this difference is maintained when you lower everything by a fixed amount.
The difference is just more pronounced after lowering because instead of, say, previously a 100mm gap between tyre and arch at the back and 70mm at the front... you now have 60mm and 30mm gaps. (Now the back is double the front, so it looks more of a difference) (?) Just a thought.