Thanks for posting!
I'm unable to reproduce this behavior. I created a new folder, changed the permissions so that it's owned by the fmserver user and the fmsadmin group and set it to be the additional database folder. This validated without issue and, after rebooting, the database opened automatically.
Can you reproduce this issue with nothing but one new database in the additonal database folder?
Do you see anything in the FileMaker Server event log to indicate an attempt to open this file? You should be able to view the event log through the Log Viewer section of the admin console.
The Server Events log file does not give any indication of opening files other than in the default location. The additional database folder files are listed and shown as "closed" in the admin console Databases status window.
I have verified the folder and file permissions to be fmserver user and fmsadmin group and the additional folder link is validated in the admin console.
The FM Server V11.0v3 and default location are installed on a solid state drive and the additional database folder is installed on a SAS drive. I ran another test where I made the additional database folder on the solid state drive and it opened those databases automatically. Does this mean the additional database folder cannot be on another disk?