OK this is interesting - I just went to Dr A's site (it's changed - haven't been there ina while) and there is a Q&A on the fiber deduction question.

He answers the question stating that some fiber is undigestable by the body, etc etc. and then goes into detail about the subtraction of those fiber counts to a net carb count - but only in the context of Atkins manufactured low carb products!!! He even gives sample labels of one of his product lables and how he reports the net carbs.