Full battery charge/with spare tire???

Lately I have been having trouble getting a full charge in the battery. It charges to all but the last line. The other day I got a flat and drove 50-60 miles with the spare tire. I had a full charge almost the whole time the spare was on! Now I have four new tires and am back to not quite a full charge. Anyone have any idea why the small spare would help me get a full charge when I otherwise can't get one?