Hi,
There is a newer version of the datasheet (28-Jul-11), but the information about that did not change.
I also checked the errata sheet for the AT91SAM128 and didn't see anything relevant.
Maybe we should check if a pullup on PA0 fixes the other board that had troube with SAM-BA, and if it's the case, just add it ... better be safe than sorry IMHO. (even if it's troubling not understanding _why_ ...)
Cheers,
Sylvain