Hi,
I don't see a reason why the Masters will not be considered.If you have seen the points calculator or the application where it asks for formal education it does not calculate based on the type of education rather is is based on the number of years.
You may very well see if there is a NOC which applies for your present occupation.I personally do not think that there should be any issues. However, this may be confirmed only by someone who has had such an experience. CIC does not state anywhere the points for science, arts or commerce it only has the NOC's for these streams of occupations.I don't think any one would know how the points were calculated for their application except when CIC comes forward and elaborates.
I hope this helps.Don't worry go ahead and do it....may be you'll be the ice breaker on such issues!!!! I feel U can and U should apply.
All the best,
AP