I try and do everything with a system account or scanning credentials and the odd cases where it has to be as a user, however its annoying dos box that pops up generates some calls, they could have resized that or displayed a message.
The way I have been doing it is to create a asset group (front page), call it in our case SOE Deployment.
Then under scheduled deployments I list that group and every package that should be deployed.
Then when I want to install a bunch of software, I add that asset to the group, re-scan the asset which will trigger the scheduled deployments, once you see them in the deployment tab then remove the asset from the group so it doesn't keep deploying.