It could be that you didn't get as much flavor with the pellets as you do with the cones, but I doubt it. I've never noticed a flavor difference between pellets and cones.
I don't use hops as much as most homebrewers do, malty beers are my thing. So when I get C hops they tend to hand around for quite a while in my freezer. That said, I've only twice ever had to throw away hop because they got too old and lost their goodness. And for one of those, I was not very happy with the freshness of the bag of hops when I first got it. So hops can go bad, but if you keep them well (as I know you must), it would be a very rare thing. I'm guessing they were sub-par hops to begin with. Especially as these were pellets. Cones don't last as well as pellets do.