Kdrown,
To my knowledge, a battery with a shorted cell will not take a charge. Your post seems to assume you know the battery has a shorted cell but you are asking if your problem could be elsewhere.
Maybe I don't understand. If you know the battery is bum then that's your problem. If you have an electrical problem and aren't sure of the origin, then it could be the battery or it could be something else. To troubleshoot this deal, you need to keep an open mind and prove each component OK as you go down your check list. You will eventually come to an item that isn't OK and you have found your gremlin. Does this make sense?
Stuart