I suspect it's the "right clicking" that's causing the multiple restorations from the deleted mail. It's not necessary to "right click" to restore a deleted email message. Just click on it, hold it, and drag it to the in box and drop it there.
try to drag the one you want to restore, from the right pane, rather than the middle one* - if you click on the body of the message and move your cursor to the top, it'll change into a little hand, you can then move the message to desired folder.
* Assuming you didn't tick 'Use classic layout' under Preferences | Viewing
Thanks, this worked better.