Take heart that some of the tears may be tiredness and adjusting to all the transitions which have taken place: likely, earlier bedtimes, earlier mornings, having to be a participant in school all day. She misses you because being home with you means that she has different expectations to meet, she gets more playtime and she has your attention.
None of these are bad things to miss. Add to this the fact that she may or may not have her buddies in her group, or some friendships may have changed over the summer.
I would give it a month or so, and then if you are still seeing distress, talk again to the counselor. Sometimes, kids get into the habit of getting upset at certain transitions. At other times, there is something deeper underlying their upset. I have nannied for a lot of families during back to school times (and my own son, included) and have seen that this transition back to schooling can take a while. This is why I suggest a month. At some point, she's going to get to know the routine, the kids in the class, and that no matter what, you aren't keeping her home from school. This experience will help her to get back on track.
Unless something significant has happened recently which you think may have contributed directly to her shyness, I would give things a little time. I've also observed that the times around birthdays, developmentally, can be tough, so I wonder if that might not factor in somehow, too, and perhaps this is how it's manifesting.
Good luck-- I hope things improve. Be patient.