What My Cloud firmware version are you using? The older v4.x or the newer v2x? Where is the media not being recognized? The My Cloud Dashboard, or the Twonky Media Server Administration screen?
Have you made any changes to your My Cloud using SSH?
Have you tried accessing the Twonky Media Server Administration page, navigate to Advanced and first select the Clear Cache button, then the Reset to Defaults button, then the Restart Server button then the Rescan Content Folders button?
Have you tried performing a 40 second reset on the My Cloud using the My Cloud reset button on the back of the My Cloud. No user data is lost rather the My Cloud is reset to default values.