CI checking permitted URI chars....in a perl script?!?!

[eluser]CroNiX[/eluser]
And I'd bet your perl script is also calling CI in places to generate things, perhaps using CI's views and that's probably where the uri characters are coming into play. It's not technically in the "uri" because it's being executed via CLI (or via web call), but that's what the built in phrase says regardless as it's checking what is passed to it in order to determine what the controller/method/params are to execute (aka the "uri").

Rereading your 2nd post, I think what I just said could be occurring in this secondary php script you say isn't using CI. Are you sure it's not a rigged bootstrap for running CI on the CLI? CI 2+ has built in ways for running on the CLI, but to get it to do it with earlier versions you had to have an extra bootstrap to process parameters (which is in turn calling CI's regular index.php and sending the controller/method/vars to it after setting some needed $_SERVER settings). Have you taken a closer look at this secondary php script that perl is calling? You might check to see if it's similar to this: http://ellislab.com/forums/viewthread/218538/#1008547