Christian,
No, this is absolutely not related to SetupBuilder. A VMWare virtual machine is a software (file) that behaves just as a physical computer does. It is a software emulation of a computer. So from the technical point-if-view, a SetupBuilder "compatibility" issue is impossible. And I don't think that it is a VMware related problem.
BTW, we are using VMWare for more than 8 years.
Friedrich