This is especially funny since the JR Pass cannot be purchased by residents of Japan.

I've also had issues topping up my (virtual) Suica card late at night before.

Yeah this is probably downstream of the fact that if you visit any of the individual JR sites from the expandable map at the bottom, you'll discover they're all down at this time as well. Let's scrap the website and make a staffed phone line or fax machine with operating hours.