If you couldn't just transfer database files, you can script your database (script table definitions and table data) and run SQL script on your target server.
I wrote DB scripting tool just last week :-) I did no comprehensive tests but that tool scripts properly table field names, primary, secondary and unique keys, auto_increments, "not null" limitations, default values and I think you will find no bugs at all in table data scripting.
I transferred my site ( http://www.mh-sd.com) using my scripting tool without any problems.
My tool was written in Perl under UNIX. It produces .sql files which you will be able to import on any platform.
I could send you this tool by e-mail (i didn't published it because it was not tested, bu I think it could help you).
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www.mh-sd.com
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