Here's what you need to do to get automation working.
1. Open iVI's Preferences, choose the Video Sources tab and select a source folder for iVI to check for files.
2. Open iVI's Preferences, choose the Automation tab and select the appropriate settings for you (say check every sixty minutes and convert all files)
3. Ensure none of the files you'd like to be automated are shown in the main iVI window. iVI's automation will ignore files the user has loaded manually assuming they are being worked on.
4. Restart iVI.
As long as iVI is running the automation should work.