Not sure on that one. I have used RB on windows 10 on all my test system when I purposely go and break something in the registry so i can test a repair and I restore the registry to continue where I left off. I havent had the problems you reported and so far I havent had anyone else say they have.
But that doesnt mean it isnt happening, their might be an unknown variable we are missing.
Thing is I am not sure why that would happen, if you use the VSS backup in RB it will copy the registry files from the shadow copy and done. If it uses the fall back method, which uses the API RegSave and is the same API erunt uses, then it calls the RegSave api and asks Windows to save the registry sections to new files. Windows then writes them out to the backup folder. This also helps make the registry files smaller since the registry is a database and just like any database it gets junk in it and grows large. Writing to new files slims that down.
Then when you restore it is the same, it uses the RegReplaceKey api to tell Windows the new registry files to use and Windows takes it from there.
So the only thing I can think of is one of the registry files isnt being restored after the reboot. On the settings that are lost, are they settings that are located in the user profile registry hkey_current_user?
Shane