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?
This is probably too late to be of any use to Massimo, but i thought i would mention that i managed to get this to work, admittedly through a somewhat forced procedure:
Here's my write-up of the process: http://libertysys.com.au/blog/p2v-of-windows-server-2008-from-efi-gpt-to-vmware-mbr
Take a look at this thread, particular the last post by BizCon Alex - http://communities.vmware.com/message/1695451
P2V conversion with EFI/GPT will be a nightmare unless someone comes out with a clean solution.
EDIT: the other option is to use a commercial product such as DoubleTake Move (http://www.visionsolutions.com/Products/DT-Move.aspx). Replicate the VM using their sync tool and 'fail-over' across to the new server.
Or if your gpt disks are not system drives (just file shares, etc.) you can just use the 4.3 version of the converter which does not get hung up at that error message and not uncheck the GPT disks from conversion. Then move them over once it is done. In our case the GPT drives were iSCSI drives that reconnected once the server was converted.
Just wanted to add another option to this thread: I performed another migration just like this a few weeks ago. This time, i used the following process:
There was no messing around with the MBR, partition table, or boot loaders. It just worked. The only disadvantage of doing it this way over VMware Converter is that it must be done offline rather than on the live server, and copying the whole disk means that thin provisioned disks don't really achieve much. If you're concerned about the latter and you're planning on expanding once you virtualise, create the VM at the original server's size, then expand the drive after the P2V is complete.
I suspect all of this will become pretty irrelevant soon, since surely an EFI-compatible version of converter mustn't be far away given how easy this process was.