When deploying from a windows 7 template the VM will sysprep it's self and then auto login with the Administrator account but it just sets there and doesn't run the run once commands that I have that points to batch files. All ideas are welcome.
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I've had similar odd experiences with this type of operation as well. I have one line in the RunOnce portion of my customization spec that runs perfectly for manually adding a new route to a secondary NIC, but the second line never seems to fire off where I restart the machine. I've tried any number of variants of shutdown, powershell Restart-Computer etc., but it never seems to fire.
I'm still working on it and you're not alone.
I'm having the same issue as well, specific to a new Linked Clone pool in Horizon View.
The above link (step 10) suggests referring to Microsoft for RunOnce command information for SysPrep, although I haven't been able to find good documentation from Microsoft about this as yet.
I'm working proactively on this issue at the moment and I'll share any new information that I find; but in the meantime any advice would be appreciated.