I have an SQL file containing two tables with around 600,000 rows altogether. Yesterday, I tried to import the file into my MySQL database on Fedora 16, and it took over 2 hours to import the file. On my Windows PC it took 7 minutes. My Linux and Windows machines have exactly the same hardware. A couple of my friends tried it too, and they had a similar experience.
The command we were using was:
mysql -u root database_name < sql_file.sql
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.