I sometimes have issues with message engine not running. Usually I'll just try to restart the whole system and hope that it goes away.
If it doesn't work, in most cases, it is caused by a corrupted file store used by the message engine and the suggestion from the Internet is to delete these files, which seems to work fine.
Sometimes, with the message engine uses a database store, I had a very similar issue. I find it quite hard to find out the exact root cause. So I chose the easier path by simply deleting the whole message engine, create a new one, giving a new schema name for the data store. This ensures it creates new tables when message engine is initialized the first time.
Creating a new message engine and re-assigning bus destinations usually take less than 5 minutes, and it seems a lot easier than troubleshooting and finding the root cause of the issue.