Is this only about Windows, or are you syncing between different operating systems? If yes, then please specify what they are, because there is a big difference between the desktop, when the application can run and sync in background, and e.g. Android, where sync is only possible when the app is open.
Not sure about the other issues, but this is normal when sync hasn't finished yet. Once everything has been synced 100%, then notebooks should appear as well. If this is on Android, you need to make sure that the app is open and the screen is turned on until the synchronisation is complete.
It’s worth noting that if something has not worked properly on your first profile, if you then just change the sync to point to a different sync target, the issues may persist. So when you say you have tested every sync option except Joplin cloud, to properly test the other options you should make a jex export of all your data, create a new profile, import the jex file and then set up sync to an empty sync target (if you already synced with it before on the sync target, then your notes will be duplicated).
Also if you have actually tested every other sync option, and you have tested Joplin server, the experience for Joplin cloud will be equivalent to Joplin server, providing you have set up the server correctly