Why would only CI be affected?
I have installed and tried others including CakePHP and Symfony. CI so far is the only one that requires the '?'.
Many other forums claim that other hosts have not had a problem with it, and that it was only seen as an issue on DreamHost. Whether thats true or not... I don't know for sure. But that being said it doesn't seem as though it would be a CGI issue. I am sure many other hosts run PHP as CGI.
Its not really a huge issue. It's just a '?'.