I know this post is almost a year old, but, seeing as how there have been a lot of views, I thought I'd venture a solution even though my situation was slightly different.
The bottom line: In CFBuilder, go to the Servers view and right click on the local server running you are running against. When the initial screen comes up, check to make sure all of that is correct, then click NEXT. On the next view ("Local Server Settings") there is a path for the Document Root. Make sure that's correct and click Finish.
The background: I had to relocate my Apache server to a new directory with a different name. Even though I changed all of the associations in the Projects and the Workspace and the httpd.conf file for Apache, the localhost settings in CF Builder were still pointing to the old Document Root. Once I corrected that, everything worked like a champ.