Ha, Just after I posted the first question I fix the problem :P. Oh well...
Reply if you wish (if you can give me some pointers).
Here is the 'fixed' code:

#!/usr/bin/perl
use strict;
my $stripped = ".command";
my $cmd;
my $cmd_loc=index($stripped,".");
my $cmd_locend=index($stripped,chr(32));
if ($cmd_locend > 1) {
    $cmd=substr($stripped,$cmd_loc,$cmd_locend++);
} else {
    $cmd=substr($stripped,$cmd_loc);
}
print $cmd."\n";
[download]

God I feel stupid now :)
^jasper <jasper@wintermarket.org>