Ahh, the old scrunched-and-munged-up-geometry-while-rigging problem. OK. The last time this happened to me I did this and it worked.
Make sure your character is in it's default pose (da Vinci pose for example). Make sure all bones are on and go through every bone and re-record it's rest position. Use the "Record Bone Rest Position" tool under Setup -> Modify -> Orientation.
Not sure if the bones have to be on or not but this should fix it.
Good luck!
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