I'd prefer MD to add the files to the end of the queue, and not resort/rewrite/refresh.
Please excuse me for the delay.
We are trying to improve this in the next build.
In the meantime you can change the sort column.
Also, you can change the Mass Downloader Options | Download | Startup | "When download completes, start the next Project using" to "Download Priority position". This will make Mass Downloader not updating the queue position every time you add the new Project.