Fresh media server install (tried twice) has old server data and odd behaviors

As mentioned, that setting can take time to update so it may have still been enabled. If you try a clean install now, it should not sync the old played status.

I reenabled the setting right after my Ubuntu install.

Why did you re-enable the setting? I thought you didn’t want things synced up with plex.tv?

I just want a clean slate

We do not currently have a way to remove the synced status from plex.tv. If you disable the feature and wait long enough before a clean install, it won’t re-use the info. But if you re-enable that setting, it will come back.