I had this problem after I moved my iTunes library to an external drive. I got libraries everywhere. Once it even created a new library on the hard drive when the external drive was attached! I had closed the lid on the MacBook with iTunes running, and when I opened it again apparently iTunes woke up before the external drive did - so it started downloading stuff into a new library on my internal hard drive. Weak. It's a crazy mess. Now I basically have to quit iTunes every time I shut the lid.
Also some of my podcasts (also "solid" ones - This American Life and RadioLab) changed things like the exact name of the podcast or the podcast URL. Apparently this is enough to create a new instance in iTunes.
More tips are on this discussion (but my brain glazed over about halfway through):
http://discussions.apple.com/thread.jspa?threadID=2617801&tstart=15
I really wish iTunes would add "show duplicates" for podcasts, not just for music. The only way I know to fix this now is to manually delete the files and then go through the iTunes interface and wait for it to notice the file is missing (it's even willing to play the podcast from the trash, apparently!) and then fix that by hand. What a pain.