In programming, as in everything else, to be in error is to be reborn.- Alan J. Perlis
When I first installed Podcast and just let it go to town importing all my postcasts, subscribing and autodownloading it completely broke background sync services. The first consequence of that was my device could not download anything. Any download would get put in the background sync queue and never download. Podcasts wouldn't download. Apps wouldn't download. WiFi Sync never activated either. The worst part was the sync services would never let the phone go to sleepy mode. So the battery would die after about 6 hours. It took a while to correlate all this crazy behavior with the install of the Podcast app.
I wiped and restored the entire phone. I subscribed to all my podcasts on my computer and sync'ed them to my phone. Same issue. I turned off the auto-download feature for all of them. No fix. I wiped and restored the entire phone. I subscribed to all my podcasts on the phone. Same issue. I disabled auto-download feature. SUCCESS!
So there you have it. Pretty simple really. Just wipe your device and restore. Then subscribe to all your podcasts directly on the device by DO NOT turn on the auto-download feature. Now all you have to do is go into Podcasts every day or so for it to show you what new shows you have to download and you must download them.
There are still a couple problems. If you don't turn on autodownload you can't turn on auto delete. So Podcast will sync all your podcasts to your computer and keep old copies of everything you've listened to. You have to go in manually to delete them. The other interesting thing is that really old episodes (3-6 months old) will randomly show up in the list as new and unplayed. So those need to get deleted.