Your assignment to $counter is never executed at the right time because you do a next before it gets encountered. And if the 'if' is false, there shouldn't be an assignement to $counter but an increment. You probably want this:

while ( <DNAFILE> ) {
            
            if (/fixedStep chrom=chrX start=(.+) step=1/) {
            $counter = $1;
            next;
            }

             print "$counter\t$_\n";
             $counter++;
            
close DNAFILE;
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Code is untested.