So, Paul, you're just noticing it now only after switching to all pellets or since switching to your new badass system? Seems odd that pellets would cause such a noticeable difference. But, having never brewed with whole hops or leaf hops, I guess I don't have any authority on the subject.
I have noticed a difference in using a hop sack in the boil versus just tossing them in and letting them roam free. Hop sack gives less of the flavor and aroma characteristics, in my experience. But perhaps it's because I was doing that in conjunction with fermenting in cornies, which I've read that the geometry of them changes the final flavor, somehow.