We aren't sure what order the flashes are written. When you have the game write normally it writes two separate 64mb files to each simm. When you manually write a simm you need to combine the files to be a 128mb file as it writes it all at once. When you write it manually using the SuperBIOS it tells you exactly what part of the file is being written. So when there is an error there it freezes on the location that it as writing. What could be done is to write a good flash, then desolder every chip and read them. Then compare the data to the original simm file to see what memory addresses are being written to which chips. We haven't done this yet. If someone would do that it would make things so much easier.
Currently when a simm is bad I just resolder the whole thing quickly. A lot of times that fixes it but it would be awesome to pinpoint the exact chip to focus on.