First off I would like to say thanks for all the replies and suggestions.
I've never had the problem you described and I have a standard bottom entrance and an entrance between the brood nest and honey supers on all my 15-20 hives. I use an excluder and place a 3/8 strip above the excluder on the back and sides.
I am thinking that I will try to go to a middle entrance and this will solve the problem. I have never used an excluder except for temporary management of a colony, like trying to locate a queen in a more restrictive area for making splits or requeening.
How do you make your top entrances? How much do they use them?
I take a piece of exterior plywood cut large enough to accommodate a 1"x2" strip nailed around 3 sided, the 2" strip nailed on vertically around the 3 sides creating a telescoping top on 3 sides. then I lay the 1" strip flat on the same 3 sides creating gap [actually about 5/8"] along one side [the front] which serves as the entrance. The front actually has no 1"x2" strip except from the flat 1" strip which runs down each side.
An alternative you can try later is to make a frame similar to an inner cover or wood-bound excluder above your excluder with a 3/8 to 7/16 entrance in the front. This will allow direct access to the honey supers and entice them to fill the lower super as you have them arranged now. A porch or landing board is optional. It is more what we think they want and not what they need. If you add the landing board you might as well add an awning and welcome home mat too! It makes a great conversation piece.
I don't use queen excluders, but if I get what you are saying what you are referring to is a middle entrance, which is what I will probably be going to with the division coming between the brood box area and the honey super area. Also mine seem to do just fine with the top entrance without a landing area, awning and also the welcome home mat

, but thanks for the suggestions.
Try turning the super around (180 degrees).
I did this and when I harvest this week I will let you know what I think about what difference it made, that is if I can remember to get back here.
Turn the entrance reducer to the smallest opening. This will encourage use of the upper one.
I don't use entrance reducers on my top entrances, and also, they use the top entrances just fine. Some do have both top and bottom entrances currently; although I will be closing the bottoms after the flow is over. I have all screened bottoms so circulation should not be a problem.
I am seeing comb bridging from the top of the brood box to the bottom of the super frames right through the excluder.
I see this generally in the brood super areas but not so much in the honey super areas, but they do create burr comb between the top super and the top entrance cover. I know that the 5/8" gap is probably to much.
Kindest Regards
Danny