I had exactly the same problem of not being able to run VMware Workstation machines whilst Hyper-V was running. You will also find problems if trying to run MS Virtual Server 2005 or VirtualPC 2007 at the same time as Hyper-V.

For all these problems I found a simple solution of booting Windows Server 2008 without the hypervisor by creating an extra entry in the boot loader. Here's how:

  1. At the command prompt, type the following:
    bcdedit /copy {default} /d "No Hypervisor"
  2. The above command should say: The entry was successfully copied to {guid}.
    Copy that guid to the clipboard including the curly braces.
  3. Now, type the following command:
    bcdedit /set {guid} hypervisorlaunchtype off

    In the above command, replace {guid} with what you copied in step 2. The
    above command just sets a property in the boot entry that will not load
    the hypervisor on boot.
That's it. If you now boot your machine you will get a boot menu with an extra option.

Credit goes to http://blog.baeke.info/blog/_archives/2007/12/18/3416738.html