I don't quite understand what you are doing here, but generally you ought to avoid nested loops. I suspect this for-for-for can be achieved earlier, when you are first building %records.

But as you have it, confirm what is happening with temporary print statements before each of your assignments:

   if (int($colLens[$x]) < length($rec1)) {
      printf "colLens:%s, rec1:%s\n", $colLens[$x], $rec1;
      $colLens[$x] = length($rec1);
      ...
[download]

Also, stylistically, instead of:

   for (my $y = 0; $y <= $#header; $y++) {
      $colLens[$y] = length($header[$y]);
   }
[download]

Consider:

   @colLens = map length, @header;
[download]

I look forward to your final, working program!

Update: I also meant to say, you have int(length(...)) in a few places. length returns an integer, so no need to wrap it with int.