Your analysis is correct. Sdclient and vulscan uae a mutex to keep out of each other's way. Here's one thing you could do: before installing any SW packages, stop the local scheduler service (net stop "intel local scheduler service").
Not a perfect solution. but we created a new landesk agent that had no scheduled scans or autofix enabled. Then last step of the provisioning task is to update the agent to the corporate desktop agent we have set.
Anyone else have a different solution. I will also look at stopping the service.
Thanks to you both, I will do some further testing and see what works best and report back.