First things first. You need:

use strict;
use warnings;
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That will never fail you.

To address your problem it looks like you are comparing against the wrong variable in your if statements:

if($string =~ /# __START_CONFIG__/i) {
    $action=2;
}
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Should be:

if($value =~ /#\s__START_CONFIG__/i) {
     $action = 2;
}
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(I substituted your space for the \s pattern instead, I like it better though if you strictly need a space, I prefer [ ] instead, that's a matter of style, I just like to be very explicit, and it tells me later that I meant to put a space in the pattern. See if these things help.