Wish I had an answer for you, but iTunes syncing has become a mess for me as well.
It ignores my settings, and syncs outdated podcasts back onto my iOS devices, downloads some only on my iPad, and some only on my iPhone, and won't automatically download new episodes on my Mac most of the time.
I also keep getting the message for one or two podcasts after each download saying it has stopped downloading episodes of those podcasts because I haven't listened to them in some time - when I have listened to them without fail for years.
iTunes and the Podcasts app are in dire need of attention from Apple.
Same problem here, Mavericks, both Mac Pro, IOS 7.4 and iTunes 11.1.3. I have some of my podcasts set to the 10 most recent. Each morning I used to sync my iphone 5s to get new podcasts. It shows up in the list on podcast on phone but when I click it says unable to access the podcast from itunes right now but showes it present. I have to delete it and download via WIFI to make this work. And previous podcasts that were in the last 10 are suddenly the same -- cannot play due to problems with itunes? Affects videos (TV shows) on my iPad same way.
Sometimes in a sync of several items some will sync and be downloaded to the iOS device others do not.
This has gotten to be a royal pain. I am forced to just do my downloads to my IOS devices via WIFI and forget the syncs to my Mac Pro.
Not good Apple.
Thanks for the replies. Your descriptions are exactly what I'm talking about. I download app updates on my device and then after synching, itunes still wants to download them and vice versa. Same with podcast issues. It stops updating podcasts that I listen to every day because it says I don't listen to them.
I think this is all about their effort to force everything to the cloud. My calendar has been a total mess as well because it can't properly sync. I'm sure a lot more that I just haven't noticed.