Yeah, I thought the log you posted in the OP was from a JB install and boot up effort. I'm not saying you should reinstall JB just for this, but if you ever do, I would be interested to see the output from the list command. And wouldn't mind seeing a secondary list from /data as well.
Here is the results of the command with the JB ROM after flashing and letting it boot loop for 10 minutes, then a battery pull, then into Recovery and the command entered.
Compare the beginning of the 2nd lines. ICS has another W
C:\android-sdk-windows\platform-tools>adb shell
ls -l~ #
ls -l
drwxr-xr-x 2 root root 0 Jan 1 00:00 boot
drwxr-xr-x 4 root root 4096 Sep 6 2012 cache
-rwxr-x--- 1 root root 245720 Jan 1 1970 charger
drwxr-xr-x 3 root root 0 Jan 1 00:00 data
drwxr-xr-x 2 root root 0 Jan 1 00:00 datadata
-rw-r--r-- 1 root root 2631 Jan 1 1970 default.prop
drwxr-xr-x 11 root root 1640 Jan 1 00:00 dev
drwxr-xr-x 2 root root 0 Jan 1 00:00 emmc
drwxr-xr-x 2 root root 0 Jan 1 00:00 etc
-rwxr-x--- 1 root root 98724 Jan 1 1970 init
-rwxr-x--- 1 root root 1415 Jan 1 1970 init.rc
dr-xr-xr-x 95 root root 0 Jan 1 1970 proc
drwxr-xr-x 3 root root 0 Jan 1 1970 res
drwx------ 2 root root 0 Jul 21 2012 root
drwxr-x--- 2 root root 0 Jan 1 1970 sbin
drwxr-xr-x 2 root root 0 Jan 1 00:00 sd-ext
lrwxrwxrwx 1 root root 11 Jan 1 00:00 sdcard -> /data/media
drwxr-xr-x 15 root root 0 Jan 1 00:00 sys
drwxr-xr-x 3 root root 0 Jan 1 1970 system
drwxr-xr-x 2 root root 0 Jan 1 00:00 tmp
-rw-r--r-- 1 root root 272 Jan 1 1970 ueventd.goldfish.rc
-rw-r--r-- 1 root root 3825 Jan 1 1970 ueventd.rc
-rw-r--r-- 1 root root 1656 Jan 1 1970 ueventd.tuna.rc
~ #