Thank you for your post.
Since this used to work, something has changed.
Once the server has started, are you able to open ALL files that are listed as Closed?
If you move ALL the files from the additional default folder to the primary default folder, do the files open automatically?
Have you tried uninstalling and reinstalling FileMaker Server?
If you can let me know what troubleshooting steps you have taken, it may help narrow down possible causes.