Why is the output.cgi converting my special characters into HTML encoded messages?

I'm writing software which sends ASCII messages that are interpenetrated by a machine via UART from my web application. The application is on the chip fine, it sends the ASCII I write via output.cgi, and I snoop on the RX and TX with realterm so I can see the strings being sent and the CGI file is the only thing interacting with my ASCII before it goes on the wire. So when I send 'RESPOND?' I can see the string RESPOND but the question mark is converted to html encoding and what is printed is 'RESPOND%3F' so my machine can not interpret this.

Has anyone had this issue or does anyone have any solutions? I have NO idea why its happening and I believe I am unable to write my own custom CGI files for the chip.

Thanks