Check the voltage across each battery with and without the charger connected, do the without test first. All batteries should have almost identical readings. Immediately after using the cart, VERY CAREFULLY check and see if any of the wiring or battery terminations are HOT. Call whoever installed the batteries if you find differing readings between batteries, or any hot connections. The next item to check would be excessive current draw to the motor, for this you would need access to a DC clamp on ammeter, mine is no where high enough rating for this application.
Hope this helps.
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Pennsylvania, for 60+ years, most recently, Allentown, now TV. 
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