File system inaccessible as root, but works fine as user

I'm quite new in the Android development scene. Recently, I installed a custom KitKat ROM and I encountered a strange issue. It is related to my SD cards (one is somekind of "virtual card", it is the actual phone storage: sdcard 0; and the other one is a real sdcard: sdcard1).

The problem is that if I "check" the root explorer option in my file manager I can't see any files from the SD card (possibly the entire system?), but if I uncheck it I have no issues. Thinking it might be a problem of my file manager, I downloaded the "Terminal Emulator" application from the Play Store and tried a simple experiment "ls" with and without executing "su" before. Whenever I execute "su" I no longer see the file system. I tried the same using "adb" and I've got same results.

without "su":

shell@IQ4410:/storage $ ls -l
ls -l
drwxrwx--x root     sdcard_r          2014-12-28 16:17 sdcard0
drwxrwx--x root     sdcard_r          2014-12-28 16:08 sdcard1
drwx------ root     root              2014-12-28 10:42 usbotg
shell@IQ4410:/storage $ cd sdcard0
cd sdcard0
shell@IQ4410:/storage/sdcard0 $ ls -l
ls -l
drwxrwx--x root     sdcard_r          2014-12-28 01:10 Android
drwxrwx--- root     sdcard_r          2014-12-28 16:08 DCIM
drwxrwx--- root     sdcard_r          2014-12-28 13:22 Download
drwxrwx--- root     sdcard_r          2014-12-28 16:08 LOST.DIR
drwxrwx--- root     sdcard_r          2014-12-28 15:23 System Volume Information
drwxrwx--- root     sdcard_r          2014-12-28 10:38 WhatsApp
drwxrwx--- root     sdcard_r          2014-12-28 16:08 com.facebook.orca
drwxrwx--- root     sdcard_r          2014-12-28 09:47 media
drwxrwx--- root     sdcard_r          2014-12-28 16:17 yahoo

with "su":

root@IQ4410:/storage # ls -l
ls -l
drwx------ root     root              2014-12-28 10:42 sdcard0
drwx------ root     root              2014-12-28 10:42 sdcard1
drwx------ root     root              2014-12-28 10:42 usbotg
root@IQ4410:/storage # cd sdcard0
cd sdcard0
root@IQ4410:/storage/sdcard0 # ls -l
ls -l
root@IQ4410:/storage/sdcard0 #

Thank you very much!

L.E. I used an app from the Play Store called "NextApp SDFix" thinking that it could help me, it didn't.