This happens no matter what option I choose (auto bone weights, bone etc.) however, this does not happen when I apply the armature directly as a modifier. I would just say oh well and deal without the auto weight but the object I’m rigging is a really long dragon and it would take too long to do the weighting from scratch. Thanks for the help guys!
u have to apply scale to the armature. ctrl + a -> apply scale. although blender shows the scale as 1 1 1, i guess that maybe some of the internal matrix are different. Maybe that matrix are used in other way when apply the weights, and have scale bigger than one.
anyway, it solves the problem.