I am not quite sure what you mean by "Try running test on native OS in both cases w/o VM."
Run it without a virtual machine. The Ubuntu 6.10 disc can be used as a LiveCD. In this case though, the performance issues seem to be with the host operating system, so if anything running Linux on bare metal would only skew the numbers more.
If you were having problems with the Linux side I would offer my help, but unfortunately I don't have much experience debugging or tuning unmanaged applications on Windows.