When you apply MD5 (or any other checksum generator) to these files on both platforms, do you get identical results?
I am not sure how much platform dependent code sits in the DBF units, so there may be a bug that only rears its ugly head under Linux....
Finally, the 2 cents you did not ask for:
Using SQLite for single user or something like Firebird, PostgreSQL, MySQL for multi-user will certainly benefit you in the long run, rather than clinging to outdated stuff with many known limitations.