You need to read the file into a single scalar, not an array like this:

my $file3 = do {local $/; <FILEHANDLE>};
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and then use:

my $response = POST (URI, [ form_zone => $file3, submit => 'Submit', 
  form_result => 'true', menu => 'edit_dns', 
  user => 'username', auth => '*:strange_string',
  account => 'account_name', mbox => ''],
 REFERRER => LAST_PAGE);
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Try this to see what did you actually pass to the POST() function:

my $aref = [ form_zone => @file3, submit => 'Submit', 
  form_result => 'true', menu => 'edit_dns', 
  user => 'username', auth => '*:strange_string',
  account => 'account_name', mbox => ''];
print "( '", join("', '", @$aref), "')\n";
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Do you see what happened? The whole @file3 array was flattened into the array in the square brackets.