I highly suspect a bad termination or cable connection at one of the jumpers that connects the batteries in there configuration for series/parallel to obtain the desired output voltage for the carts 48 volts. If one of the terminals is loose or bad, you loose the whole string. This would prevent the charge circuit from charging. What is the output rating 48 volts DC? Using a DC volt meter, check the voltage at the main output and see if it's correct. That would be a starting point. If it's correct, it could still be a connection Tug and wiggle each wire jumper wire at the connection and post, looking for a loose wire either on the post, or in the terminal.
Let me know what your finding are and we'll go from there.
How many batteries are there?
What is each battery rated voltage?
You could have one of these connections to get the 48 volts, depending on whether they use 12 or 6 volt batteries:
All it will take is one bad connection
at one of the jumpers