[eluser]TheFuzzy0ne[/eluser]
I have to say, I'm a totally baffled. I don't see how any of those characters should be disallowed. The fact the page is rendering in the browser certainly suggests that it's being run twice. I would suggest enabling logging and checking the logs to see if that really is happening. Obviously, that's to satisfy my own curiosity more than anything - I doubt it's the solution.
I can't help thinking that your Perl script calls CI, which calls a Perl script, which calls a PHP script, which again calls CI.
Can you confirm that there's really only one CodeIgniter application there, and not two that are running from different code bases/configurations?
I think this just goes to show how important it is to comment code so the poor sod that inherits it, doesn't wake up at random intervals at night screaming "NO MORE CODE!!!", eventually falling back to sleep again whilst weeping into his pillow. I hope, for your sake, someone got demoted over that.