There is a "cursed" item in the Cursed Abbey that will drain your stamina constantly if it is in your inventory(it doesn't even need to be equipped to cause this drain). The name of the item will give it away.
This may seem like a stupid question, but do you perhaps have the 'always run' option on? You may have accidentally hit the key that activates this function.
I hope that either of those two situations are the case.
