Internal resistance within the battery. Take a good voltmeter and check when your batteries are under a good load to see the voltage across each battery top. If you find the single battery is dropping more than half of the full voltage from end to end, try moving that battery to a parallel spot and see what happens. Each battery will have somewhat close to six volts across it's tops, but if after moving the arrangement you find the single battery is less than before, it's a sure indication that battery you suspect is indeed causing problems.
With a little creative wiring, perhaps you won't have to move the batteries, just the wiring.
