You need to use a lookahead instead. Without that each s/,,/whatever/ eats up 2 commas so the 2nd and 3rd comma in a row in the original text are never tested. Here's a solution:

my $sql = "'XXXX-ax1-d.ett.amrs.bankofamerica.com','UAT','AMRS','AMS',
+'','YYYY','ZZZZ',,,,";
print "$sql\n";
        $sql =~ s/,(?=,)/,NULL/g;
print "$sql\n";
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