Such bugs are common in Microsoft software. You do have alternatives such as GoodSync, SyncBack and others.
I setup folders on two drives to sync - like this
G:\MyFolder .... H:\MyFolder
and somehow Synctoy switches drive letters on me
H:\MyFolder .... G:\MyFolder
My G Drive is the source and H Drive is the destination
why is it doing this - i deleted all the sync pairs and the sync files in each folder- and then recreated all the pairs again - yet it still is swapping drive letters