I am trying to get old episodes of podcasts accessible through iTunes and on my iPod. However, when I add these episodes to the "Automatically Add to iTunes" folder, they get automatically added, but to the wrong place - they are not getting classified as podcasts (despite their detailed info showing that they belong to the podcast genre). How can I get around this such that they get classified / filed as podcasts?
You'll have to modify the metadata to specify the media kind as "podcast". The easiest way I know if is by using iTunes.
However, you could possibly use an applescript to automatically do it. I'm by far not an applescript expert so I'll leave that part up to you.
You will need to use an app like Subler or MetaX to directly alter the embedded tags. Setting the meta data through iTunes doesn't persist if you then transmit the file to another computer.
After you add them to iTunes: Go into iTunes, select each one of the files(I think they'll be in the Music Library), right click->Get Info->Options tab. Set the Media Kind to Podcast.