90 megs is not that much. The smallest size where I would expect you to have problems is 2 GB. Maybe you're just misreading the file info from one of the OS's?

Try this experiment to see if there is really a problem: copy the file Win2000, on Win2000 rename the file, then copy it back. Then on SCO,
do:
wc old new
diff old new | wc -l

That should tell you if there really is a problem or not, thus answering your last question.