Same here with the badass tokens not working. I've also noticed that the health gets damaged with certain big damage but it doesn't affect the shield when both the the health and shield cheats are on using Maya.
I haven't noticed the Badass tokens yet but I have indeed noticed the health drain with Gaige so I do not think it's one character type but all of them.
I will have to test the tokens later tonight and see if the same thing is happening for me.