These courses will not be counted in your GPA, regardless of what your transcript says. If you read the AMCAS rules about calculating GPAs (part of the official AMCAS handbook, which is available on their website), you'll see that courses taken P/F, C/NC, etc. are excluded from the AMCAS GPA. I had a couple of these courses on my own transcript, and the AMCAS reviewer recorded them as zero credit hours. This didn't mean my school didn't give me credit, just that AMCAS didn't use them in its calculations.
I don't think the AMCAS application will let you leave a field blank, so you'll have to enter something there (I would advise a zero). Regardless of what you enter, though, if your transcript looks the way you describe it, I bet AMCAS will change it to a zero. (This kind of change is considered a routine correction and doesn't count against you.)
I don't think this issue is going to affect you at all. First of all, grad grades go into a separate GPA bucket, and frankly get almost no attention from med schools. Second, even if anyone did care about your grad GPA, you're better off with P/F excluded if the alternative is to assign it a point value other than 4.0. (Some colleges, for example, assume that P is equivalent to a C for GPA purposes.)
I have an MBA degree from a school that gives H/HP/P/LP/F grades, which according to the AMCAS website is equivalent to ABCDF. But the person who reviewed my transcript changed them all to P/F, which resulted in a grad GPA of NA. Regardless, I got into med school anyway.