I have noticed podcast bookmarks getting "lost" on the iphone since updating to IOS5. Turning OFF wireless syncing over WiFi seems the correct the issue, but I'm not certain yet. Will do some more testing today.
Example: A podcast I listened to conclusion yesterday, was marked as "unlistened to" in iTunes after a wireless sync. As soon as I turned OFF wireless syncing (in iTunes, for the iPhone) and synced over the cable, the podcast wass correctly marked as "listened to".
Looks like wireless sync isn't the issue. I was listening to a podcast when a call came in. After I ended the call, the podcast started over from the beginng instead of where it left off.
Also noted that the NEXT episode of a given podcast does not automatically start anymore, as it did in the previous IOS.
I have also been having issues syncing podcasts with my iPhone 4 since updating to iOS 5. When syncing over wi-fi it's common for the podcasts on my iPhone to not be updated. I often have to revert to using the USB cable and on occasions this has also failed to work with the solution being that I have to remove all podcasts from my iPhone and then add them again. I haven't noticed any problems with my iPad other than unplayed podcasts not being marked as such. Though this seems to be a removed feature. Another error I have found is when downloading a new podcast episode from iTunes using my iPhone. The podcasts fail to sync to my MacBook and just sit on my iPhone until I manually delete them.
I much simpler solution would be to have podcasts controlled by iCloud and have them sync across all iOS devices. I'm sure this is in the works and will come along soon and was hinted as much during beta testing of iOS 5. I for one find myself often having to turn my MacBook on just to update my podcasts subscription to my iPhone/ iPad.