1) Yamato, unlike some other ships of its class, has a different registry for its saucer section and battle section, possibly alluding to the fact that it spends more time separated than together for some reason.
2) Yamato's logs were corrupted before they were beamed to Enterprise in the first place, which explains the odd registry (it's just sort of a random number dropped in there, part of the Iconian program's attempt to access the ship's navigational codes).
Just my two cents here about the different saucer... I really have a hard time with the idea that Galaxy Class saucers are interchable without some modification... As ships are build, systems are never completely the same. And I say this because of what must be a significant primary mission of a ship as it's commissioned for construction, even though of the same class.
On the other hand, I have no Trek evidence to support my vews. They are simply what I envision in this case.
I would lean more towards supporting file corruption.