Here is the proper procedure:

http://line6.com/support/docs/DOC-2223

its a design flaw.... the sensor gets dust on it and stops from registering 0... you physically need to open up the pod to clean the little disk.... its not hard or anything but obviously not for everyone to attempt.... there was a post about it somewhere on here

mine was doing the same on the first calibration after powering up. Toe down 255 and then the heel down was only rolling back to 20 instead of 0. Found if I pushed D to save it, then went back into it again by pushing VIEW and ran thru it all again, it worked the second time.