[T-Mobile Samsung Galaxy S II SGH-T989] RealPariah:
Script to flash via CWM to fix fix perms has been done by minotauri (sorry if miss spelled will fix when on a computer) he deserves credit for the edify:

To Run Fix Perms While in Recovery Flash this file each and every time you need it run [for now]:

http://goo.gl/hrL7E

The Next Script is one you can flash via CWM and it will replace the file ROM Manager uses so this will remain between restarts and you can use it via ROM Manager or Script Manager anytime you want!:

Thank Minotauri again for another beautiful Edify!

http://goo.gl/qPpC3

Flash via CWM and it well work for that flash just flash anytime you need to run it via recovery until I see about permanently copying it over existing script or still can run manually with this guide if you choose [scroll down below the additional update on how to fix the script to run using ROM Manager while in OS!].

I posted this in a couple ROM threads and was asked to throw it out here as folks from different ROMs are all affected. I can only speak for TMobile Galaxy S2 as that is what I own, drive and work on...

I will be cleaning up the post a bit when I get time just want it posted so others can use the information add it really seems to help clean up small issues (even some report fixing multiple FCs after running fix perms this way!)

NEWEST UPDATE 2012.04.19

OK FIX FOR RUNNING FIX PERMS INSIDE OS VIA ROM MANAGER

If you adjust first line in script to #!/system/xbin/sh viola ROM Manager does not freeze [finally]

I did this with Ghost Commander [don't forget settings> check auto root] and long press fix_permissions and choose edit tapping it will have GC try to execute it.

I also moved down to set variables piece and placed 1s instead of 0s next to mount system, mount data, and remove (as in REMOVE stale data :) ) [should be all caps in /data/data/com.koushidutta.rommanger/files/fix_permissions

I am still working on finding a way of making those changes permanent in /sbin under recovery boots

Fix Permissions Work Around ICS

Run Fix Permissions via ADB Shell with Phone in Recovery

I have taken the time to document what should be a complete guide to running fix permissions while the phone is in the Recovery menu using adb.

I am posting the quick steps right after this, but if you scroll below that this is an extended step-by-step guide.

Running Fix Permissions

On Phone: go in to Mounts and Storage Menu from Main Menu and choose to mount /data and /system
On Computer: type adb shell
This should give you a ~# prompt
Now type "sh /sbin/fix_permissions -l -r" [without quotes]
and now you should see a bunch of text scroll by and then it will say fix permissions completed blah when done.
that's it type exit and hit enter about 3x [one will change ~# to ~$ then it will drop back to C:\blah and then one more time will close that window as well

Supplies [Phone, USB Cable and Android SDK (http://developer.android.com/sdk/index.html)

Follow the link to install Android SDK [they have directions on site]

first time installing adb? [Skip otherwise]

To Add ADB to your computers path [to run it from any directory]

Windows:

Open Command Prompt [Click Start, Click Run, Type in cmd and hit Enter [XP]]

Open Command Prompt [Click Start, type cmd in whitebox and hit Enter [Vista and 7]]

type set PATH=%PATH%;C:\android-sdk\platform-tools [or wherever you put android sdk just add platform-tools to the end [it is a hidden folder]

Linux [OSX should be same]:

PATH=$PATH:/home/user/android-sdk/platform-tools [or adjust for where you saved it]

export PATH

Now That You Have ADB and path set, time for good stuff

Opening a Command Processor

Open a Command Prompt [Windows] or Terminal [Linux or OSX]

Windows: Click Start, Click Run, Type cmd and hit enter [XP]

Click Start, type in to Whitebox cmd and hit Enter [Vista and 7]

Linux: Hold alt and hit F2 on keyboard [should see a run box now]

Type in xfce4-terminal and hit Enter [or substitute your terminal command this is xubuntus]

Once a Black and White Screen Opens...

Gaining Elevated [Admin or Root Privileges]

Ok, some further testing shows me you should have root or admin access to command processor before running ADB.

In Windows

Type The Following in to the command prompt window already open...

runas /user:%computername%\administrator cmd

hit enter when done

[yes just like that including %computername% windows will fill it in with proper info copy/paste if needed right clicking in command window should paste text for you [if not right click on the icon in left hand corner of title bar choose properties and place checks in the quick edit and insert mode boxes under Options tab]

now it will ask for a password if you have not set one you need to go to control panel users and set a password on admin account before this will work

Once you enter the password and hit enter a second command window will open and will have Administrator in the title

Now You can continue on

In Linux

With Terminal window open type:

gksudo xfce4-terminal& [sub your terminal command if not using xubuntu]

once you hit enter it may take a second but you will get a password prompt enter in your password and a new terminal will open and it will have Root@ in the title

Now you can continue on...

Checking USB Connection

type in adb devices and hit enter

[if you get a command not found you will have to use cd to move to directory with adb [ie cd c:\android-sdk\platform-tools]

If it comes back with ?????? as serial number it is not connecting correctly follow the next steps otherwise skip the next bit if you didnt get all ?

I get ?????, what gives?

This seems due to not running command prompt or terminal as administrator or root user [Windows / Linux Respectively]

You will need to do the following in order

Disconnect USB from phone

On Phone: In Advanced menu choose restart recovery

On Computer: type in adb kill-server and hit enter

Reconnect USB cable

Be Sure To Follow Section above labeled: Gaining Elevated [Admin or Root Privileges] and then continue on

On Computer: type adb devices and you should see a mix of letters and numbers

and that means we are good to go on

Running Fix Permissions

On Phone: go in to Mounts and Storage Menu from Main Menu and choose to mount /data and /system

On Computer: type adb shell

This should give you a ~# prompt

Now type "sh /sbin/fix_permissions -l -r" [without quotes]

and now you should see a bunch of text scroll by and then it will say fix permissions completed blah when done.

that's it type exit and hit enter about 3x [one will change ~# to ~$ then it will drop back to C:\blah and then one more time will close that window as well

Device: TMobile Samsung Galaxy S2 [SGH-T989]

ROM: Yaldak's Vanilla ICS RC2

Radio: Blaze ICS

Performance Mod: Supercharger v6 update 8

Client: Xparent Green TapaTalk [latest]