Default Missing directories when viewing on pc

I just got my first LG for my son. I have rooted it already but I noticed something and wondered if anyone else has this problem.

The problem is when you view the sdcard through browser on the phone the files are all there but
when you plug it up to the usb port there are some directories missing. What gives? I looked at the
permissions and their all not "hidden" but yet the directories aren't in the pc browser...

Also, does anyone know of a app that looks like something else that I can hide app icons in so they can't be seen in the app window... I have some apps that run in the background of my sons phone that allows me to know what he's up to without making him feel like he's on a leash. Trust but verify ya know. lol