When characterizing don’t put the Root bone into the Reference Slot:
instead put the Root bone into:
Then click Characterize, then in Character Settings make sure Hips Translation Mode is set to World Rigid.
Select the Root bone then go to Window/Open Property View, under Root Bone in the Properties /Degrees of Freedom/Translation, tick
Enable Translation DOF
and under Min T, tick
Enable Min Y
(this seems to stop the Root bone going under the floor – it never seems to go above the floor – possibly using Enable Max Y would sort that out)
Then plot to skeleton, I think you can leave Plot Translation on Root only unticked.
In UDK in the Unreal Anim Set Editor Under Properties/AnimSet leave Anim Rotation Only unticked. Playing the anim with Skeleton selected should show a purple line from 0,0,0 to the floor under your characters hips