Perhaps the software you're using has an Endian disagreement with the Motorola 68000. (IE, perhaps the software assumes little-endian hi/low, in which low would be the first physical byte, but the Mac ROMs assume "high" is the first of each 16 bit word.)
As long as you're correctly getting even/odd byte distribution you should be fine burning your ROMs with it split either way, it's just the terminology that's confused. Just plug them in after flashing and if they don't work first time swap them.