[Galaxy S II Q&A, Help & Troubleshooting] desean:
Hi [MENTION=3445281]pedestre[/MENTION],

My CWM SU will be removed and SuperSU reinstalled each time I reboot my phone. Currently on 4.6 Light TWRP. Here are my logs:

user.log.bak

Wed May 22 21:45:07 SGT 2013 START of post-init.sh
grep: /system/etc/tweaks.conf: No such file or directory
/sbin/post-init.sh: line 30: //Cargar: not found
mount: mounting none on /acct failed: Device or resource busy
mount: mounting none on /dev/cpuctl failed: Device or resource busy
/sbin/post-init.sh: line 73: can't create /sys/kernel/debug/sched_features: Permission denied
Extraer payload
1540+0 records in
1540+0 records out
788480 bytes (770.0KB) copied, 0.106428 seconds, 7.1MB/s
rm: can't remove '/data/app/Superuser.apk': No such file or directory
rm: can't remove '/system/app/Supersu.apk': No such file or directory
rm: can't remove '/data/app/Supersu.apk': No such file or directory
rm: can't remove '/system/app/*supersu*': No such file or directory
rm: can't remove '/data/app/*supersu*': No such file or directory
Copiando las liblights
mkdir: can't create directory '/system/Apolo': File exists
Wed May 22 21:45:09 SGT 2013 PRE-INIT DONE of post-init.sh
Wed May 22 21:45:21 SGT 2013 Default Value 50
Wed May 22 21:45:21 SGT 2013 No .enable_crt so 50 is default value for fb_pause
Wed May 22 21:45:21 SGT 2013 USER EARLY INIT START from /system/etc/init.d
Wed May 22 21:45:21 SGT 2013 USER EARLY INIT DONE from /system/etc/init.d
Wed May 22 21:45:21 SGT 2013 USER EARLY INIT START from /data/init.d
Wed May 22 21:45:21 SGT 2013 USER EARLY INIT DONE from /data/init.d
Wed May 22 21:45:21 SGT 2013 USER INIT START from /system/etc/init.d
START 'S999pegasusqsio'
EXIT 'S999pegasusqsio' (0)
Wed May 22 21:45:52 SGT 2013 USER INIT DONE from /system/etc/init.d
Wed May 22 21:45:52 SGT 2013 USER INIT START from /data/init.d
Wed May 22 21:45:52 SGT 2013 USER INIT DONE from /data/init.d
Wed May 22 21:45:52 SGT 2013 END of post-init.sh

user.log

Wed May 22 21:51:34 SGT 2013 START of post-init.sh
grep: /system/etc/tweaks.conf: No such file or directory
/sbin/post-init.sh: line 30: //Cargar: not found
mount: mounting none on /acct failed: Device or resource busy
mount: mounting none on /dev/cpuctl failed: Device or resource busy
/sbin/post-init.sh: line 73: can't create /sys/kernel/debug/sched_features: Permission denied
Extraer payload
1540+0 records in
1540+0 records out
788480 bytes (770.0KB) copied, 0.090707 seconds, 8.3MB/s
rm: can't remove '/system/app/Superuser.apk': No such file or directory
rm: can't remove '/data/app/Superuser.apk': No such file or directory
rm: can't remove '/system/app/Supersu.apk': No such file or directory
rm: can't remove '/data/app/Supersu.apk': No such file or directory
rm: can't remove '/system/app/*supersu*': No such file or directory
rm: can't remove '/data/app/*supersu*': No such file or directory
Copiando las liblights
mkdir: can't create directory '/system/Apolo': File exists
Wed May 22 21:51:37 SGT 2013 PRE-INIT DONE of post-init.sh
Wed May 22 21:51:49 SGT 2013 Default Value 50
Wed May 22 21:51:49 SGT 2013 No .enable_crt so 50 is default value for fb_pause
Wed May 22 21:51:49 SGT 2013 USER EARLY INIT START from /system/etc/init.d
Wed May 22 21:51:49 SGT 2013 USER EARLY INIT DONE from /system/etc/init.d
Wed May 22 21:51:49 SGT 2013 USER EARLY INIT START from /data/init.d
Wed May 22 21:51:49 SGT 2013 USER EARLY INIT DONE from /data/init.d
Wed May 22 21:51:49 SGT 2013 USER INIT START from /system/etc/init.d
START 'S999pegasusqsio'
EXIT 'S999pegasusqsio' (0)
Wed May 22 21:52:19 SGT 2013 USER INIT DONE from /system/etc/init.d
Wed May 22 21:52:19 SGT 2013 USER INIT START from /data/init.d
Wed May 22 21:52:19 SGT 2013 USER INIT DONE from /data/init.d
Wed May 22 21:52:19 SGT 2013 END of post-init.sh

S999pegasusqsio in the log is my own init script which contains this:

#!/sbin/busybox sh

sleep 30

# governor and io scheduler
echo "pegasusq" > /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor
echo "sio" > /sys/block/mmcblk0/queue/scheduler

# pegasusq tweaks
# Pegasusq settings from http://xdaforums.com/showpost.php?p=26488751&postcount=425
echo "90" > /sys/devices/system/cpu/cpufreq/pegasusq/up_threshold
echo "95" > /sys/devices/system/cpu/cpufreq/pegasusq/up_threshold_at_min_freq
echo "40000" > /sys/devices/system/cpu/cpufreq/pegasusq/sampling_rate
echo "2" > /sys/devices/system/cpu/cpufreq/pegasusq/sampling_down_factor
echo "5" > /sys/devices/system/cpu/cpufreq/pegasusq/down_differential
echo "30" > /sys/devices/system/cpu/cpufreq/pegasusq/freq_step
echo "100000" > /sys/devices/system/cpu/cpufreq/pegasusq/freq_for_responsiveness
echo "10" > /sys/devices/system/cpu/cpufreq/pegasusq/cpu_up_rate
echo "20" > /sys/devices/system/cpu/cpufreq/pegasusq/cpu_down_rate
echo "400000" > /sys/devices/system/cpu/cpufreq/pegasusq/hotplug_freq_1_1
echo "200000" > /sys/devices/system/cpu/cpufreq/pegasusq/hotplug_freq_2_0
echo "350" > /sys/devices/system/cpu/cpufreq/pegasusq/hotplug_rq_1_1
echo "200" > /sys/devices/system/cpu/cpufreq/pegasusq/hotplug_rq_2_0
echo "0" > /sys/devices/system/cpu/cpufreq/pegasusq/ignore_nice_load
echo "1" > /sys/devices/system/cpu/cpufreq/pegasusq/io_is_busy
echo "0" > /sys/devices/system/cpu/cpufreq/pegasusq/max_cpu_lock
echo "0" > /sys/devices/system/cpu/cpufreq/pegasusq/hotplug_lock

# Apolo extra setting
echo 1 > /sys/class/misc/notification/notification_enabled
echo 1 > /sys/class/misc/notification/blnww
echo 0 > /sys/class/misc/notification/breathing
echo 0 > /sys/class/misc/notification/notification_timeout
echo 0 > /sys/devices/virtual/sec/sec_touchkey/force_disable
echo 0 > /sys/class/misc/notification/led_timeout_ms
echo 2800 > /sys/devices/virtual/sec/sec_touchkey/touchkey_brightness
echo 0 > /sys/devices/virtual/sec/sec_touchscreen/tsp_slide2wake

#AWAKE_MIN="200000"
#AWAKE_MAX="1000000"

#scaling cpu freqs
#echo $AWAKE_MIN > /sys/devices/system/cpu/cpu0/cpufreq/scaling_min_freq
#echo $AWAKE_MAX > /sys/devices/system/cpu/cpu0/cpufreq/scaling_max_freq

# UV
#echo "1275 1175 1075 975 950 " > /sys/devices/system/cpu/cpu0/cpufreq/UV_mV_table

Thanks for checking.