Could be a few reasons:
- If you created an exclusion filter then it would miss files (probably not the case)
- If you have any other backup programs that run and then auto archive files or delete them.
- A possible cron job that the hosting provider runs which could have possibly moved/delete files
- Possibly a caching system that cleaned itself up
- You may have had a file that was readable by the PHP process duplicator runs under and the permissions got changed which then didn't allow the plugin to archive the files..
Usually if its half the size then something large was removed on the site. The only way to really identify the differences is to use a tool like Beyond Compares Directory diff tool. Extract both packages then do a diff on them. http://www.scootersoftware.com/
There is a 30 free trial which should let you test.
You might try to create 2 or 3 packages back-to-back and see if something is going on in your server that is causing the plugin to not archive the data correctly...
Hope that helps!