(copy pasted from another thread that dealth with a similar issue)
I used to have lots of problems with the unity supplied character controllers. this caused an error because of rigidbody, that caused an error because of god knows what else.
I resorted to skipping past all unity controller whatever, and making my own with playmaker. and as a bonus, I now know why something does or doesn't work, or how to change anything easily.
so...
put you a capsule or a 64x128 sprite up there, and make it move with get axis or axis vector, and translate or add force, im pretty sure I use set velocity sometimes, but maybe just with sprites. im not too sure about the specifics but when its set up correctly, its much easier to tweak it to act like you want it to.