That is expected. The config file user-dirs.dirs masks the true directory names so that the stock file manager will call them something else. What exactly depends on your theme and language. For example for me, the DCIM folder is called Camera. .sounds is called Audio Clips etc.

I am a bit concerned that your ~/.config/ contains only five items. Mine contains 34 including hildon-desktop, osso-calculator and tracker. I wonder how customized your device must be to work without those.