iTunes 11.1 introduced some huge changes, specifically with regards to podcasts. You may not realize it, but podcasts are now synced with your iOS devices (and Apple TVs updated to Version 6) and that means iTunes manages things VERY differently. From sorting to deleting, nearly all of it has changed. We'll be talking more about that on our upcoming Mac Geek Gab this Sunday, and likely writing some more tips, too, but for now there's a great post at Apple's Support Forums with some good tips to get you started. Hopefully this helps!
Check It Out: 8 Great Tips for Managing Podcasts in iTunes 11.1