Have you checked the system chart for the flattener (p. 15 of the manual linked below)? The recommended image train is the Camera Angle Adjuster, SD ring (optional), flattener, wide T-mount, DSLR.
http://www.takahashiamerica.com/manu...C%20Manual.pdf
It sounds like your back focus is too short (i.e. flattener/camera is too close to the OTA) when you have the flattener attached - possibly because you're missing the CAA? - but too long when you add the extension tube in with the flattener.
From memory, I think there wasn't much spare travel in the focuser on my FS-60CB with the recommended flattener configuration.
The easiest way to check for sure would be to centre your scope onto a bright star, leave the OTA bare (i.e. don't attach anything to the focuser), have the flattener attached to the wide T-mount/DSLR, look through the DSLR viewfinder and slowly move yourself closer/further away from the OTA until the star snaps into focus. That will show you what the required distance is - and you'll be able to figure out whether you're too close/far from the focus point.