I agree with Michael Bush (as I very often do - he has extensive knowledge and hands-on) which can differ from single-hived bee yards, but your bees are driven by instintual traits and NOTHING can break their actions (other than extreme intervention by us) so give her time and she will be moving up.
Better stated, in milder climates, people may only keep ONE SUPER over winter, so there is no "UP" to to go! But keep in mind the weather and when cool weather generally comes to your area and work with that.
Make sure the upper super is filled with frames that are full of honey and when the time is right, everything will happen as it should. Remember too that queens (as all honeybees) are always active, even into the cluster during the coldest days of Winter - so there are always "things to do" in the hive and each warm day gives the bees another chance to PERFECT their Winterization of the hive and the queen may be staying low JUST to keep out of the way.
Lastly, think of that last statement as like when the PRESIDENT comes to the stricken areas of the US Southern States, you need to change what you are doing to accomidate his trip - when the queen comes to the honey supers, it is telling the REST of the hive that something different is happening and the WAY THINGS ARE DONE are about to change to "Shuffle" multiple tasks in this NORMALLY queenless box (that goes whether you use excluders or not) so have patiences with the hive, all should work out fine and honeybees RARELY have a poor sense of pre-Winter preparation!!!!