Hi,
It's normal for a charger to act like that with completely dead
batteries.  It can't charge until a little resistance builds up.  That
charger is probably connected to the whole battery bank.  It's possible
if you left it on long enough and it didn't kick it might have started
charging.  But getting a little charge into each battery is faster and
more likely to work.

I don't know if you know how batteries are wired but here is an
explanation.

If two 6V batteries are wired in series then you have one 12V battery.
If three are wired in series then you have one 18V battery, four equals
one 24V etc.  Batteries wired in series adds the voltages.

If two 6V batteries are wired in parallel then you sill have only 6V,
but the amps double.  Three wired in parallel sill 6V but three times
the amps, etc.

If you have two 6V batteries wired in series connected in parallel to
two more 6V batteries wired in series then you have 12V and double the
amps of one battery.

So with 6 batteries you can have voltages from 6 to 36 volts depending
upon how they are wired.  When you connect two batteries together in
anyway you no longer have two batteries but one.  If you connect all 6
together you have one battery and the charger needed to charge that one
big battery depends upon it's voltage.   You should find out what the
voltage is for the battery bank in the golf cart, the six batteries
connected together.

If you charged two 6V batteries wired in series with a 12V charger you
did right.  In fact that's the voltage it has to be to charge both
batteries.  As long as those two were separated from the others or wired
in parallel with them.

The only thing you did wrong was letting the batteries go completely
dead.  That shortens their life span.

Hope this helps.  Take care and Happy Campin...