Testing processor performance

I have been trying to test cpu performance using Nbench and have found
that I get better results running XP on VMWare system using a quad
core than I do on an XP system running a dual core AM2 5200+ or
5000+ . I clocked the same system with the two different processors
and was only able to obtain results about half of what I was able to
achieve on an XP system running in VMWare on top of a quad core 9850
linus system. For measurement I was most interested in Floating point
and Integer MOPs/sec.
I originally saw the problem when running a database program and found
out it was five times slower on the system running on system A running
directly on dual core vs system B running in VMware on a quad core
9850. The VMware system has only one CPU allocated to it.
When I realized I had a problem, I suspected first the hard drive,
then the MB, then the CPU. All have been changed out, along with the
memory.
Any ideas on why I am seeing this difference? I just feel like there
is something I am not understanding here. I don't really want to
install a quad core into a system when it is only utilizing one CPU