Apparently the way TS3 is being 'killed' when you stop the server is incorrect. When the server is stopped it doesn't communicate with the TS3 accounting server - thus accounting assumes you still have the server running (for 3 hours after the server is shut down) until it times out.

If your ts3 server is not properly stopped (for example because you used kill -9 / kill -kill), the accounting server is not told to release the slots the ts3 server was using. Only after 3 hours since the last report of that server, will the accounting server time out the improperly stopped ts3 server instance and release those slots. Although in most situations, the accounting server is able to recognise a server restart, and you don't have to wait 3 hours.
- by Teamspeak Team member Too many slots hosted, shutting down!

This is causing a lot of issues - specifically after updates and such...