Whenever VSE is disabled, check the Event Logs for "McLogEvent" entries that have an ID higher than 5000.
5000 = Scanner is starting.
5001 or higher = a problem.
Once the problem is identified you can evaluate what action to take.
The most common cause, a fatal scan timeout has occrred (5019/5051) on a specific file - which could be a product issue to investigate, or something to exclude from scanning, or ignore if you think it's a one-off occurrence.
Hotfix 638179 is something highly recommended for your VSE version.