Not really. You should never use the Auto Defect setting. This defaults to MTP mode, but can also connect in MSC mode if conditions for MTP are not just right (different computer, phase of the moon, etc.).
If the files were originally loaded in MTP, then that would be why your computer cannot see them if connected in MSC mode. The reverse is also true, files loaded in MSC mode cannot be seen while connected in MTP.
It sounds like your files were loaded in MTP mode. You should manually set the USB Mode to MTP. Again, it is not advised to use the Auto setting. 
