My bet is that Fedora 16 is honoring the transaction/sync semantics and Windows is not. If you do the math, 600,000 updates in two hours is 5,000 per minute. That's the same order of magnitude as a disk's rotation rate.
You can try adding SET autocommit=0;
to the beginning of your import file and COMMIT;
to the end. See this page for more information.
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