I'm rather ashamed to even have experienced this situation but I did.. and I figured it out for myself..
I got to work in an application that relied on client variables heavily.. So, not having the time to rebuild the application, any changes I made or subsites of it relied heavily on client variables..
I had a situation come up one day where I set client variables and although I could output them in the same document (application.cfm), I could not in included documents, the document that called application.cfm or onrequestend.cfm.
After some frustration, I was ready to start over, I went to the top of application.cfm, ready to highlight the <CFApplication> tag and found out the problem.
I didn't include a name of the application so variables would not carry beyond their local environment, no matter WHAT I felt like naming them..