I seem to have this issue too.
This is sooo annoying along with another problem that I have, it seems the setting in iTunes not to sync podcasts does not stick.
I only listen to podcasts on my iPhone, never on my MacBook. This is now the third time, at least, that iTunes syncing messes up my podcasts list completely! Podcasts I have listened to appear as new, Podcast episodes I have deleted manually from the phone appear again, and I believe some of the episodes I have not yet listened to disappears. This happens even if I immediately after connecting the phone go to the Podcasts section and uncheck the "sync podcasts" option. And yes, sync podcasts is also turned off in settings on the phone.
This unfortunately makes me avoid backing up my phone.
Is there some logic here that I am missing? Or some setting that I have not discovered?
iPhone 5s, iOS 7.0.4, Podcasts 2.0.1, old MacBook with OS X Lion and iTunes 11.1.4 (62)