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[eluser]IAmThePat[/eluser]
Well, after looking a bit more, I found on the bitbucket repository for CI, a bug report similar to this issue, which fixed my problem.

I am using the default controller to catch the query string. Apparently to do this though you must have the default controller in the URL in order for it to work.

Example:
http://mysite.com/welcome/?test=nice -- Works
http://mysite.com/?test=nice -- Fails

Thanks for your assistance, and getting back to me
-Pat