Sounds like you have a rifle that was dry fired a lot and the nipple is mushroomed over.
The Seneca uses a nipple with a 12-28 thread. I would give Cain's a call and order up a replacement nipple from them and a wrench to fit. They make both. Their Spitfire nipples are pretty good.
Actually, most any of the muzzleloading catalog houses could help you with the items: Track, Dixie, Log Cabin, Gun Works, etc.
That is a sweet little rifle you have. Enjoy.