I got a Jalapeno plant that produces those funky ones, too. My biggest pods aren't even that big (1" @ most). I might call it quits for this Jalapeno plant.
What I did was pick off the smaller one(s) and allowed the plant to concentrate it's energy on the existing bigger pods. You probably already know this, but if you touch the pod and the skin feels smooth and hard that's probably the biggest it will get (and it's probably just concentrating on ripening), but if the pod is sort of abrasive and isn't smooth, it's still growing, leave it alone because it's still growing. My two cents. Does anyone else do this?