Welcome @khardman
Regarding the Global Inbox…
- Quit DEVONthink.
- In the Finder, press Command-Shift-G and paste: ~/Library/Application Support/DEVONthink 3/Inbox
- If you see the folders in here (and this is where they should be) you can safely delete them.
- Relaunch DEVONthink.
Also are you syncing and via what method?