Try disabling "Genius" on your iPhone if you have it enabled. (To do this, you need to disable it in iTunes and then sync your phone.) This seems to have fixed it for me.
This issue has been driving me crazy for months, to the point that I would delay syncing my iPhone for days so that I wouldn't lose my place. It seemed like it had something to do with the "mini-sync" that would happen immediately after I plugged in my phone (even though I have iTunes set to sync manually). If I was in the iPod app on the phone when the mini-sync happened, it would say something like "Updating library" on the screen.
I didn't know what was causing the mini-sync, so I disabled other apps that I was using that read the iTunes library (last.fm scrobbler and Lala Mover), but it still happened. The only thing left was Genius, and disabling that seems to have stopped the mini-sync and preserved my podcast markers.