I changed my HP with VIT gems and armor, and it still happens.
Happened on two separate characters, both were demon hunters, one lvl 30 and one lvl 51.
I noticed this happening last night, had never had it happen before then.
EDIT: Tested on my lvl 60 Wizard in nightmare and normal and it just hits for normal damage, doesn't stun though, maybe being too high level to get stunned by low level mob.
Also took my 51 demon hunter to normal and same thing, so I'm wondering if its the stun component thats causing the 99% hp damage.