The clean out that they do is probably just a reformat, although I'm not too sure, someone else could confirm. If it is just a factory system reformat then you could order the recovery CDs from MSI and simply do it yourself.
If the warranty is coming from MSI and not the retailer then you could contact MSI by...
MSI Computer Corp. - Contact Us
EDIT: nevermind, didn't see the multiple pages >_<