Galaxy S with Cyanogenmod 10 (stable): File Manager needs root permission to access the external SD card
Sounds like the permission for the mount point of the external sd card got messed up.

This is how it looks like on a SGS with CM 9.1:

shell@android:/ $ ls -l /mnt/ 
d---rwxr-x system   sdcard_rw          1970-01-01 01:00 emmc