Internal ROM does not write anything to NAND, so EBOOT must be modifying the boot tables in NAND for some reason. It shouldn't actually do that under most circumstances (unless you want to update bootloader), so it may be misconfigured in some way. Usually bootloader have reserved memory area to store configuration info, and this EBOOT may have this misconfigured. Not familiar with details of EBOOT though...
regards,
vladan