is she a new kitten [new to the house]?
was she socialised well before coming to her new home,and was she taken away from her mum at a late enough stage?
kittens can be very people-shy,especialy when they were not socialised enough as little ones and when they are taken away from mum to early.
if the vet has checked her over very recently,and said shes fine-dont try and force her out.
instead,let the kitten come out herself instead.
sit in the room doing something else,or outside the room but dont put any focus on kitteh whatsoever.
do not push attention on her,let her do the rubbing,this allows her to see her new human isnt overwhelming afterall and can gradually build up a trust and bond,it works very well with shy cats-sister had exactly the same trouble with a litter of kittens and mum she rescued from her works garden and the kitten woud hide under the bed to,it turned out after speaking to neighbours there that the man who owned the mum abused her and woud kick her out every time she was pregnant so she had no trust of humans and passed it onto this little one especialy through behavior.
but with this avoidance therapy,ruby [as she is called,as she kept the shyest one and the mum] has become a very confident adult,she loves her rubs and purring.
woud recommend the book that helped sister understand all this and cat behavior overall, its called the cat detective,by vicky halls [a cat expert and behaviorist]:
*click here*