So it is saving the change to the database but it is not clearing the site settings cache so it still shows the old settings until you touch Web.config which clears the cache. The only problem that can prevent clearing the cache is if file system permissions are not correct. There are text files created that are used for cache dependency so when we want to clear the cache we just touch the cache dependency file, but if it cannot modify the file then it fails to clear the cache.
So, something has changed in your file system permissions. You need to make sure the /Data folder and all sub folders are writable by the web process.
I would delete the old cache dependency files, if folder permissions are correct they will be re-created anyway.
Delete all files from /Data/systemfiles and /Data/Sites/[SiteID]/systemfiles
Hope it helps,
Joe