I know you say it is happening at start up but maybe you are doing something else? I do things automatically. In fact I press into a workspace on opening and that caused me a similar issue.
If you use workspaces DEVONthink 3 will open ones you had open when you made the workspace I think. I can’t quite remember, BLUEFROG will confirm or not. I had the same problem as you and that is what I think was causing it I found. Just close the data bases and update the workspace I think that was what I did.