Mike Kol write a nice article about managing Sysprep utility and avoid Virtual Machine Additions to be disabled in the process:
If anyone has tried syspreping Windows Vista Beta 2 inside a VM, you may have noticed that the VM Additions are still installed but not functional afterwards.
This is because of the way that the new Sysprep Generalization phase works. The idea here is that the system starts with a totally clean slate, and PnP detects the “best” driver for the hardware all over again.
For some reason, the drivers included with the Additions are not detected as the “best” fit. I’m not on the setup team, so I’m not sure why, but that’s what seems to be happening.
There are a few ways to work around this…
Read the whole article at source.