Hi twcvzw,
There are two instances where this can happen. One is upgrading to 2.0:
2.0 changes the way it reads feeds since some podcasts are starting to publish at the bottom of the feed instead of the top. So, to handle those, podtrapper now looks at not only the top episodes in a podcast, but also the bottom few. To conserve RAM on the device, PT only loads a hundred or so episodes, half from the bottom and half from the top. For the vast majority of podcasts, this is more episodes than they publish. But, some podcasts always publish every episode they've ever made, and sometimes it goes over the threshold. It's in these cases where PT will now look like it's seeing old episodes.
Once they've loaded, though, you should be good to go after that. Also, in version
2.0.2 (beta) I've added an 'Update and sort' menu item that will get them back into proper podcast order.
The other way it can happen is when the publisher changes servers or otherwise alters the URL of existing episodes. Since the only consistent way PT can see the uniqueness of an episode is via the URL, if this changes PT sees them as new episodes. Unfortunately there's not much it can do in that situation.
Hope this helps, let me know if I can answer anything else for you.
-Marcus