The problem is likely related to the cache files. Settings are cached in cache/ with files named like fc-journalSettings-*.php. When the settings are changed, OJS should delete the relevant cache, and it should be recreated when it’s next needed. If OJS can’t delete the file, you’ll see behaviour as you describe – changes will be made to the database but not reflected on the website.
Make sure your file permissions permit OJS to administer the files in cache/.
(This should result in error/warning messages – I’m not sure why you’re not seeing them in your case.)
Public Knowledge Project Team