[Q] After reboot some apps lose their settings

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Hi All, After flashing(CF-Root-XX_XEU_JPY-v1.3-BusyBox-1.17.1.tar) my phone Galaxy S GT-i9000 I am faced with a really annoying problem.
Now it seems like all of the apps that have settings that should be retained once set, are no. Every time a reboot happens, I have to go to all of those and put new settings..:(
Its really annoying can some one shed some light why and hows?

Thanks

corrupted file is probably main cause.

make a backup using Titanium or something similar. do a factory reset in recovery and also wipe cache , dalvik cache , datadata

reboot and restore