Can you confirm that non-spigot servers work?
Because if the problem only appears with the spigot server present, then I think we’ve identified the problem: MineOS + that spigot server.
If the above is true, then no, a fresh install wouldn’t help. Relocate the server away from /var/games/minecraft entirely, like in your user’s /home directory. Primarily concerned with /var/games/minecraft/servers/servername, not as much the archives/ and backup/.
If we can determine it’s specifically that Spigot instance, then you’ll probably want to share the server with me. I wouldn’t need the world files (so it should also be a small file, in general), but I would need the combination of your server jar and the accompanying mods. Then I can definitively test where the failure is happening that MineOS is stalling with.