I have been syncing an iPhone with iTunes since the phone came out. A few weeks ago I had my iPhone 3G replaced under warranty and for some reason iTunes won’t “remember” my sync options for podcasts anymore. Previously, I was able to check off which shows I wanted synced, leaving out HD shows for the ATV. Now, when I listen to shows, they are removed from the list of available shows in the iTunes to be synced to the phone and I need to manually check them off again when new shows are downloaded. Is there a way to have iTunes remember again that I always want MacAnswers (and some others) always synced if there are shows available? All software is current versions.
— Andrew Chlopik
It sounds like a setting got changed. I would carefully review all the settings in your iTunes controls for that iPhone. Something is different. Chances are that your old iPhone was using settings that were converted from pre-iTunes 9. Things synced differently then. All of those controls were different. You can do the same now, plus more, but I think something changed when you started using the new hardware. So it is just a matter of reviewing the settings. And there are a lot of them.
Just as a side note here, after the installation of iTunes 9.0.3 a short while ago, the list of available podcasts to be synced over now includes all subscribed podcasts again, regardless of whether or not there are new/unplayed episodes. Everything is back to normal again.