Restoring backup in Configurator only applies some apps

Using Configurator, I created a backup of an iPad set up the way I wanted it.

When I restore from that backup onto another iPad, only some (a few) of the apps restore into a few of the folders. Why is that?

I haven't been able to restore any successfully yet... Doing my head in. We only have 16 iPads, but surely I'm not going to have to manipulate all of the apps into correct folders for each of them? If I select the apps I want to download under 'supervise> apps' then they seem to download into the correct folder, so do I have to manually go through and select the apps again (even though they were on the ipad that I created a back up from?