Don't take this wrong, but are you confusing polished with clean?
I've got a Hornady unit, and it typically just needs one 40 min cycle to get things nice and clean. They'll look bright and shiny when you rinse 'em off, but they dry sort of dull. There might be a bit of carbon in the primer pocket, but otherwise, they're clean, just not polished.
Now if the brass is coming out dirty after an hour, there's something wrong.
Try only loading half as much in the basket. smaller loads seem to work better. Also, be sure you have the right cleaner. Hornady makes two different solutions. One for brass, one for parts. Easy enough to grab the wrong one.
You can find a lot of homebrewed solutions on line. You might want to experiment and see what works best for you if you're still not happy with the Hornady solution.