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It certainly sounds like you've done your homework in looking at ways to automatically start virtual machines on Microsoft Virtual Server. The first option you mentioned -- assigning a security context for the virtual machine and setting it to startup automatically -- is the simplest to configure. You mentioned that it is difficult to manage, but you could manage these settings programmatically through the use of VBScript and the COM API to make it more manageable.
Regarding option two, as you mentioned, startup scripts will run under the security context of the Virtual Server service. If you want to use this method, you can assign a domain account (and appropriate permissions) to the Virtual Server service. The benefit is that you don't have to worry about the order of execution (as in option three).
And, regarding option three, you could set up dependencies or use more complex code to monitor for the start of the Virtual Server. For example, you could create your own service that specifies the Virtual Server service as a dependency. (Note: I've never done this, so I can't guarantee it will work). Regardless, I think this approach is needlessly complex.
Overall, my advice would be to build a small but simple management application that uses the Virtual Server COM API to set VM startup settings.
If that's not a good solution, feel free to follow-up with some additional details on why options one and two will not work, and I'll try to help you out. Good luck!
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