Settings changed wont save after reboot

Any changes that i do in my Mac, wont save after reboot.
If i change the settings on my mouse (unchecking Scroll direction) next time i reboot, it will be checked again.
Any changes that i do to my Finder sidebar (like adding My Main Drive not visible, add downloads and pictures, change the foler view as columns) they are all gone after i reboot. Its getting freakin anoying. I Google for a solution but to find none.
When trying to opening Calender, it says that i dont have permission. I have gone to the application and checked and made sure that all acounts have r/w permissions.
On the Dock, i uninstalled an app and next reboot i will get a question mark, even tho i removed it before it comes back after the reboot.
Thanks for listening.
Burn1nator

May sound silly, but are you sure you're not logging in as the 'Guest' user? What privileges does the user account you're using have? Check in
 > System Preferences... Users & Groups
that the account you're using is Admin. If you're using a Standard account, are parental controls enabled?
If you are admin, try resetting your permissions and removing the sys pref property file. Before you do that, backup your system and user data. Once you're backed up, open Terminal and copy/paste the following into the Terminal window:
rm ~/Library/Preferences/com.apple.systempreferences.plist
hit 'return'. If the prompt returns without an error (as it should), paste this
sudo chown -R `id -un` ~
hit 'return'. Enter your password as requested, but type carefully as it will be invisible while you do.
This will take a while, but after the command finishes (i.e., when the prompt returns), restart the mac.
After the restart, set the mac up the way you want, then test whether the problem is fixed by restarting again to see if your changes were kept.

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