There are two different versions of the Ys pack-in: one printed in Japan and one printed in the US (they're labeled accordingly). More than half the titles have similar minor packaging differences that have nothing to do with game play.
Really? That's pretty cool. That's a minor difference, though. I have to look at my pack-in to see if it's USA or Japan.
I know the Turbo grafx controllers sometimes have different "stamps" on the back, molded plastic. I forget exactly what the differences is, it's something like one is just NEC, the other NEC technologies. Something minor like that.
The CD are and Pack-in CD art are pretty different though, not just small text. Very different art on each CD, not quite the same as the color swap on Champions Forever.
I remember a discussion about this many years ago here, and I posted a pic of the CD art of both. I probably still have it around here.
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Oh, not box related, but for collectors, the Dungeon Explorer 2 CD game had a reprint. Yes, it was reprinted, a normal pressed CD, complete with a Xerox copied instruction manual!
Actually, did that DE2 CD reprint have any differences?
I bought a reprint when TZD had it, but I sold it some years later after I bought a complete DE2, with the normal instruction manual and rear CD case insert.