Undesired automatic system preferences changes

Question

Has anybody experienced automatic changes of system preferences after restarting/shutting down the computer?
This is what I've been struggling with since I updated to Mavericks on a MacBook Pro 13-inch Mid 2009:
1) Trackpad/scroll direction. I prefer not to have the natural scroll, but it reverts to selected
2) Keyboard: I want the F buttons as standard function keys, but this turns to unchecked
3) Language and Region/Advanced/number separators, I want the "." for decimals, but it turns to "," (I'm Italian, but for my job it's easier having the "british" sets)
4) I prefer Google Chrome as default browser, but after restarting/shutting down, Safari becomes the standard browser.

Answer 1

If you're having trouble making changes to files that are inside your home folder (represented by a house icon in the sidebar of a Finder window), or if you can't get changes to the settings of an application to stick, then please see below.
Back up all data.
This procedure will unlock all your user files (not system files) and reset their ownership and access-control lists to the default. If you've set special values for those attributes on any of your files, they will be reverted. In that case, either stop here, or be prepared to recreate the settings if necessary. Do so only after verifying that those settings didn't cause the problem. If none of this is meaningful to you, you don't need to worry about it.
I've tested these instructions only with the Safari web browser. If you use another browser, they may not work as described.
Step 1
If you have more than one user account, and the one in question is not an administrator account, then temporarily promote it to administrator status in the Users & Groups preference pane. To do that, unlock the preference pane using the credentials of an administrator, check the box marked Allow user to administer this computer, then reboot. You can demote the problem account back to standard status when this step has been completed.
Triple-click anywhere in the following line on this page to select it:
{ sudo chflags -R nouchg,nouappnd ~ $TMPDIR..; sudo chown -R $UID:staff ~ $_; sudo chmod -R u+rwX ~ $_; chmod -R -N ~ $_; } 2>&-
Copy the selected text to the Clipboard by pressing the key combination command-C.
Launch the built-in Terminal application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Terminal in the icon grid.
Paste into the Terminal window (command-V). I've tested these instructions only with the Safari web browser. If you use another browser, you may have to press the return key after pasting.
You'll be prompted for your login password. Nothing will be displayed when you type it. You may get a one-time warning to be careful. If you don’t have a login password, you’ll need to set one before you can run the command. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.
The command may take a few minutes to run, or perhaps longer if you have literally millions of files in your home folder. Wait for a new line ending in a dollar sign ($) to appear, then quit Terminal.
Step 2 (optional)
Take this step only if you have trouble with Step 1 or if it doesn't solve the problem.
Boot into Recovery. When the OS X Utilities screen appears, select
Utilities ▹ Terminal
from the menu bar. A Terminal window will open.
In the Terminal window, type this:
res
Press the tab key. The partial command you typed will automatically be completed to this:
resetpassword
Press return. A Reset Password dialog will open. You’re not going to reset a password.
In the dialog, select the startup volume ("Macintosh HD," unless you gave it a different name) if it's not already selected.
Select your username from the menu labeled Select the user account if it's not already selected.
Under Reset Home Directory Permissions and ACLs, click the Reset button.
Select
 ▹ Restart
from the menu bar.