not heard of reprogramming a battery, but if you get a ctek 5
http://www.amazon.co.uk/CTEK-CTE-MXS.../dp/B004ZWV1JI it can recondition the battery. I had a few problems with only short journeys, on an old battery, during the cold weather, and this charger appears to have sorted it.
I'd try this first before worrying about anything else.