As discussed elsewhere, Windows Server 2008/R2 will automatically use the EFI boot loader when installed on EFI systems, and will also automatically use the GPT partitioning scheme on such systems. And you can't do anything at all about this (other than force the system to switch to BIOS, if this is supported).
But, as documented here, VMware Converter is not going to convert GPT disks. Which is actually quite suprising, when considering that it supports EFI systems and they in turn use GPT disks... but that's it.
So, how to perform a P2V conversion on EFI/GPT Windows servers?