i often have problems with MED after saving models with bones. sometimes, when i save, model totaly deforms. this is terrible, because i have been lost a lot of time with it for remodeling model!

do not save while animate mode is active

And:
Save versions of the same model from time to time. F.i. save the mesh before adding the bones. (I do this with other model tools, too.)

A third advice: Check if you have many bones with the same name. This also causes wrong animation when saving.