I've imported a design from Eagle, and I'm trying to replace the parts with verified Upverter ones. The intelligent pin mapping does a terrible job - for example, swapping out an LED results in strange routings and one of the pins being disconnected. Swapping a voltage regulator connected most of the pins to ground, and did strange things to the net around it. Swapping an ATMega makes complete gibberish.
Is this normal, or just beginner's pain?