Hi Kasi,
(Though the post is old, i recently faced this issue & my findings below)
Check the below things,
1) open TCURX table & give currency key = JPY and see if you have any entries. If yes, check the no. of decimal places to be used. This is the reason for showing the values differently.
2) If you want to see the actual value as it is posted "enable do not use any conversion" settings.
Thanks,
Bharath