Seeing performance differences on single vs multi-core

We are seeing some significant performance differences on single vs
multi-core processors on AMD chips.

We have a database application that we are running on XP which also
does regression analysis.

I have asked the manufacturer of the software if they have seen this,
but they have not. They are using Clarion from SoftVelocity to build
the application.

on some systems I know the core others I do not

AMD Athlon Socket 939 (single) 4000+ 102 secs

AMD Athlon 64 X2 (Toledo) (single) 4800+ 145 secs

AMD Athlon 64 (Unknown) (dual) 3500+ 184 secs

AMD Black Edition (Brisbane) (dual) 5000+ 780 secs
(Overclocked to 3GHz)

AMD Athlon 64 (Brisbane) (dual) 5200 +

AMD Quad Phenom 9950 810 secs

We then installed the application on an operating system installed as
guest in VMWare

AMD Quad Phenom 9950 92 secs

Any idea on what is going on here. This really doesn't make sense. I
would expect maybe a little performance hit but 5 to 6 times
different..

The only hint I can see of the issue may be the run made on the
Toledo. While it's clock speed is faster It's performance is still
worse than a 4000+. My understanding is that a Toledo is a dual core
with one core disabled.