The structure of this ROM is as follows:
3 MB on ROM SIMM
1 MB on flash chips
The ROM SIMM is not supposed to change, but the Flash chip can and did during development. This was the reason for only 3MB being checksummed: the last 1MB, which resided on the Flash chips, could easily be changed.
Therefore, the fact that only 3MB was checksummed was NOT a bug, and was completely deliberate!
What utility was used to dump? We usually recommend CopyROM from
http://www.emulators.com/freefile/MACUTILS.ZIP because many other dumpers only grab the first 3MB or otherwise scramble the dump. Would it be possible for a re-dump to be taken with this version of CopyROM, as well as a screenshot of the CopyROM window? This would establish whether the ROMs actually are weird, or that the dump was bad.
Thank you!