Basically the same thing here as well. Since upgrading my Apple TV to version 6, syncing of podcasts are hit and miss (mostly miss). Prior to version 6, I kept video podcasts on my Apple TV and audio podcasts on my iOS devices for the most part. Since the new syncing feature in version 6, my audio podcasts show up on my Apple TV about 10 or 20% of the time when displaying my podcasts.
I don't know when it actually syncs, but I do wish there was a way to manual refresh the sync. Often I will see new podcast episodes showing up on iTunes on my Mac, but not on the Apple TV.
And when they do sync, the accuracy is horrendous.
I hope Apple fixes this ASAP. I was excited to see that syncing across devices were added to version 6 of the Apple TV but I have been terribly disappointed by the results so far.