Podcast syncing changed?
I definitely feel your pain when dealing with managing podcasts with iTunes on iOS devices. With the challenges of either creating a smart playlist that I can't then order (at least I've generally found this to be impossible) or the idea of having to micromanage my podcasts through a standard playlist as well as the oddities of what podcasts get synced and why I've generally given up.

What I recommend is a specific podcasting app. There are a few out there. I started with Instacast, but it became a little unstable for me recently. I've since gone to Podcaster, and aside from the initial learning curve, I like it more. The nice thing about either of them is that you never have to use iTunes to sync your podcasts either, as they'll download them over wifi or 3G.

Sorry that I can't provide a solution directly related to your iTunes challenge, but I've been happier going this route and maybe you would be as well.