This has been haunting me this entire week, particularly since I found the solution more than once but chose to forget it. Thankfully we started this blog to help us provide the answer for the things we forget.
So, if the visual query builder does not show up when you try to edit a master page or edit detail page while using the Coldfusion Flex or Ajax application wizard, HERE IS THE SOLUTION:
Start Flex Builder as an ADMINISTATOR! (Windows Vista or 7)
I hope I will remember the next time...
To reiterate, starting flex builder 3 as an administrator fixes the issue where the Visual query builder does not seem to work while trying to edit master page.