It looks like Scott @ the Cosmology Project has got things straightened out now. The Windows Wu's run just as fast as the Linux Wu's with the new v1.20 Application. On my Quads the times have improved by at least 50% or more.
The Validation issue where when 1 Windows & Linux where paired together 1 wouldn't get Credit seems to be working much better now too. I've had no 0 Credit Wu's since yesterday even when paired with a Linux Host ... :)