Did you carefully go over the "sync list" (expanding all the branches) to make sure that there aren't other items checked that could explain the behavior? I believe the list works in an "AND" fashion, meaning that if you have "All Audio" checked, but you also have a playlist checked that contains video files, you'll get video files as well.
Exactly what do you mean when you say "sync with 1 specific podcast"? Do you mean you created a playlist that only contains a single podcast and nothing else, or that it contains a list of files that only includes a single podcast, or ? Note that if you don't have "delete all files not in sync" checked, it will keep all the current files on the iPod.
You might want to delete everything on the iPod and create a very short, simple smartlist or playlist (a couple albums), then look at the list of files that MC is planning on syncing. and see if you can isolate the problem.
Larry