[JoeyP]

The cowering is probably a result of where you got her from
and with time that will go away
but you can speed the process A LOT by making training interaction FUN
just coming to her and holding a treat over her head isn't fun to her
it probably sounds like she is being reprimanded
make the giving a treat something that is fun
get down on the floor with her and with a happy high voice give her treats and talk to her
Pet her and tell her what a Good Girl she is .... this will transform the setting and do this a few times before you start the actual training sessions
then it will be something she will look forward to and her interaction with you will be much better