Windows isn't saving settings...

[leetshoe]

So l tried to start my computer up but it said a registry file was corrupt and it wouldn't start. But then later l tried and it started up but changed my background and setting to default (like what to open a pdf with, and use the classic start menu, etc). Also l'm pretty sure my font changed. Except for that, When l ran a program it would say in the bottom right corner "C:/$security is corrupt, run chkdsk". So l ran chkdsk /f and now everything looks alright with no errors or nothing except Windows settings won't save. (but start menu settings will, and background can change)

Examples:
Can't change what default program to open file extensions
Can't get rid of basic Desktop icons (IE, Network, Computer, Control Panel, etc.)
Can't show file extensions

This is Windows Vista on a Vaio laptop. l also ran Malwarebytes and it didn't catch anything. So anyone know what to do to fix this (please use layman terms)

Also when I shut down it reverts the start menu settings