JRPass

The Japan Rail Pass effectively starts at 12:00:01AM on your first day of use, and ends at midnight (11:59:59) on the last day of use. This is the JR standard rules whether you first board a train at 6AM or at 6PM on your first day.

Key Point: the validity is counted in rounded days, not hours.

You are free to travel any time on the starting date/day of your Japan Rail Pass. it will expire on midnight of your last day, after this you cannot board a train, but if you are already on a train you can continue to your destination at no additional cost. (eg. you can use it on board a sleeper train for example, that arrives after the last day of validity, as long as you depart within the valid period)

There's more on the jrpass.com blog: http://jrpass.com/blogs/can-i-use-my-jr-pass-with-breaks-between-days