You show a very incomplete piece of code that is even missing the label cont. I'm not sure what this piece of code is supposed to do or how or where I could see that it is skipping every second line.

Please remove irrelevant parts of your code, and add the parts that show the results you get.

As an aside, please also do work on your indentation. Your code is very hard to read for me:

if (length($pais) < 1){
$pais = $cc;
$adm1 = $codes{$adm1};

if ($cc !~ /US/gi){
$adm2 = $codes{$adm2};
}
...
[download]

is much easier to read when formatted as

if (length($pais) < 1){
    $pais = $cc;
    $adm1 = $codes{$adm1};

    if ($cc !~ /US/gi){
        $adm2 = $codes{$adm2};
    }
...
[download]

That way, it becomes clear where each if block begins and ends.