what kind of model are you trying to rig?

did you get rid of a previous rigging? sometimes I get the same issue with projects I try to totally redo the rigging..
(go into hypergraph and make sure there isnt anything from previous rigging etc...) also set driven keys.. might have made an issue as well.. but Im not sure.

so now usually i take precautions in everything I do..

like after i finish the model.. I back up the file and put it some where safe, same for the fully textured version etc etc

I dunno whats ure problem entirely.. because I don't have enough information to make any judgment on the issue however.. hopefully sum1 else can help ^^