Multiple entry to/from Japan

Does three hours at the Tokyo Narita airport, waiting to change planes, constitute "entry" in to Japan as far as the Rail Pass is concerned?

I will be flying from the USA through Narita to Taipei, then coming back a couple weeks later to spend two weeks in Japan, and will want to activate my Rail Pass at that time.

When I fly through Narita the first time, I will be arriving on one airline and leaving on another, so I will need to re-check my luggage, and will probably have to go through customs — but I don't want the Rail Pass to count that as an "entry" into Japan.

Thank you.