I realize this is old, but people may find it searching for the solution. It’s that CFBuilder’s check of that server home folder looks for it to include a jvm.config file in the bin folder under that server home…which commandbox does not have.
If you just create an empty jvm.config in that WEB-INF\cfusion folder (see the original post here), that will allow CFB to let you get past that screen. (Commandbox won’t be bothered by it, and since folks would rarely look into that folder it shouldn’t confuse too many humans. 
)
If Brad or anyone might offer a point of contention on that, do let us know.