The backup is done on a background thread. There are two possible causes for this:
1. Your VM is configured to run with a single core.
2. Writing to the hard disk slows down the process.
Auto backup fires every 10 minutes. In most cases it should complete in less than a second.
Edit: The zip creation step happens on the main thread. If the project is big then it can take a few seconds to complete and the IDE will not be responsive during that time.
You can disable this feature (Tools - IDE Options - Auto Backup).
the unreal engine using a small timeout window / information for auto-save with possibility to cancel.
i remember that zip had a compression rate that affect the time for zipping all.