Your name being printed with your surname first followed by your first name is absolutely fine and will not be a problem in Japan. It's actually the Japanese way to write names surname first.
But really, as long as the names are spelled correctly and match those in your passport, the name order does not really matter. Please rest assured that your voucher will be considered valid and will be accepted by JR staff in Japan with no issues as long as the first and surnames on the voucher are the same as those in your passport.
Comments
Your name being printed with your surname first followed by your first name is absolutely fine and will not be a problem in Japan. It's actually the Japanese way to write names surname first.
But really, as long as the names are spelled correctly and match those in your passport, the name order does not really matter. Please rest assured that your voucher will be considered valid and will be accepted by JR staff in Japan with no issues as long as the first and surnames on the voucher are the same as those in your passport.
Japan Experience
http://forum.japan-rail-pass.com/discussion/comment/3045#Comment_3045