Hi Imran,
The CV-Boole is not changing the way Boole works internally, it is a management tool, it is supposed to support your work and safe time.
This special case that you have shown is perhaps one of the few cases where Boole does not deliver.
My suggestion: when you need a shape that has resulting segments all on the same “plane”, perhaps use Splines and the new Spline Tools (see image). With an Extrude applied to the result, this will allow you to even specify the created surface (Caps: N-Gone, Triangle, Quadrangles, [Grid]) where the problem with the example was before. (Perhaps even explore “CV-Splines To Objects”) Then Boole it with the sphere, given your example.
Again, this should be discussed in a new thread in the QA Forum, with a current problem. CV-Boole can’t change that.
As I think that this specific case is very well known, I’m not even certain if a “suggestion” is worth to invest your time.
http://www.maxon.net/support/suggestions.html
But it can’t hurt ;o)
All the best