I cannot answer your mysteries #1 and #2. Especially #1 sounds really weird. Are these machines really in sync now?

Joplin is not able to sync in the background. So sync will stop if the app is in the background. For daily use thats fine, but for the first sync the display has to be active (!) and the app needs to be in the foreground.

Are all your devices connected to the same OneDrive account? You can check by accessing the web interface and check the content of the onedrive folder. What does your sync status show? Does it show the right number of overall notes?