the easiest way to fix this is to delete that joint, first unparent all child bones from it and delete it and simply replace it with a new joint.

as an explination of what happened is you made a full chain of joints branching from the root. usualy you want to make your root and end its chain there then make all other chains seperate. then parrent them to the root when your finished. this keeps the orentations of the root seperate from any chain in the hierarchy so your character will have a parent orentation that is to the world.

if you wanted to take the hard way of fixing it its similar to the easy way. all you would have to do is un parent the skeleton from the root and zero out the rotations. if the orentation is screwed up you need to use the orent tool to fix it to the world. ( skeleton>orent tool = option box)

make sure your setings are reset and your rotations are zero .

if you have any other questions, IM me and I'll help you out.