I may be able to give you some help with a very common problem. I've experienced the same thing for years on several different pickups. My final solution....1. I had the bed treated to a spray in bed liner to seal all the larger seam openings. 2. Still had some dust problems, so
put in a tail gate seal (Cabelas). 3. Found some small leaks from round holes in the box corner stantions which I can see no rational reason for, so bought several household corks of various sizes, and used silicon sealant to glue then into the holes, then trimmed the ends flush with the surface. 4. After another PD hunt in South Dakota's dusty side roads showed that I was still getting small amounts of dust leakage, I talked to a local body shop about the problem. One of the young body repair specialists gave me a tube (10.5 oz) of a product called "Big Stretch" made by a company called Sashco, in Brighton, Colorado. This is just a non hardening caulk and sealer made for doors, windows, and siding. I later found that several local hardware and "big box" stores carry the product. Doesn't harden or crack, and very easy to apply. Just make sure the surface is as clean as you can get it. (I used Rubbing Alcohol with great results!) Is dry to the touch in 4 or 5 hours, and comes in many colors. After seeking out and sealing 3 or 4 small gaps with the product....no more dust or water leaks.

Now, several of my friends and acquaintances have used only the "Big Stretch" treatment on the boxes of their Chev, Dodge, Ford, and Toyota boxes with good results, they simply calked all the gaps and holes with tubes of the stuff that are close to the body color of the truck, or
clear product that actually dries "clear".

IF, you don't have a good seal on your topper or cap, your are just wasting your time trying to cure the problem of the dust intrusion!

Good Luck
Bill