www.makemkv.com

Same file size, run time, audio tracks, video codec etc but

1 title has English + multiple lanquage subtitles listed for selection

the other has English and Japanese subtitles (it's always Japanese) listed for selection

A fairly common occurrence. Why does this happen?

Because the disk authors did it that way. A lot of disks are authored such that one file contains multiple episodes, one of which has additional commentary audio. The menu on the DVD or BD will hide the fact that all of the episodes have the extra track(s).

One for Region A, one for Region B...

http://en.wikipedia.org/wiki/Blu-ray_Disc#Region_codes