To ensure it is not a wrong data handling trouble (its likely to be a write privileges problem), what about using XML for config files? For the config file, you can try something like:

<opt>
  <section1>
   <param1>foo</param1>
   <param2>bar</param2>
  </section1>
  <section2>
   <other>foobar</other>
  </section2>
</opt>

And then, use something like this to read, modify and update your config file:

use strict;
use XML::Simple;

my $config = "fooconf.xml";

my $xml = XMLin($config) or die "Error reading config: $!";

$xml->{section1}{param1} = "replacement1";
$xml->{section2}{other} = "replacement2";

open CONF, ">$config" or die "Error writing config: $!";
print CONF XMLout($xml, NoAttr => 1);
close CONF;
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