Settings reset after shutdown + popup

Question

I don't usually shutdown my 2014 Macbook Air except the occasional freeze but recently decided to do so while I wiped the keyboard clean. Once I turned it back on and signed in, I found all my preferences reset including trackpad set to 'tap to click', dock icons reset to original, etc. It seems like everything was reset to factory settings.
I tried going to Preferences to change the trackpad to 'tap to click' but discovered that it was already set do so...yet I'm unable to 'tap to click'.
The other problem is I get this annoying popup which I've never seen before titled "OSX needs to repair your library to run applications". Even after entering the correct password, the popup reappears. Then I tried just hitting cancel repeatedly until it disappeared. That's when a different popup appeared--something titled "mail chain...enter your password"--can't remember exactly.
This was all occurring on one of my user accounts so I tried switching back to the original Admin account and found the same issues occurring there (the account also reverted back to factory settings).
Any ideas? Your help is much appreciated.

Answer 1

Back up all data before proceeding.
This procedure will unlock all your user files (not system files) and reset their ownership, permissions, and access controls to the default. If you've intentionally 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, but you do need to follow the instructions below.
Step 1
If you have more than one user, and the one in question is not an administrator, then go to Step 2.
Triple-click anywhere in the following line on this page to select it:
sudo find ~ $TMPDIR.. -exec chflags -h nouchg,nouappnd,noschg,nosappnd {} + -exec chown -h $UID {} + -exec chmod +rw {} + -exec chmod -h -N {} + -type d -exec chmod -h +x {} + 2>&-
Copy the selected text to the Clipboard by pressing the key combination command-C.
Launch the built-in Terminal application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad and start typing the name.
Paste into the Terminal window by pressing command-V. I've tested these instructions only with the Safari web browser. If you use another browser, you may have to press the return key after pasting.
You'll be prompted for your login password, which won't be displayed when you type it. Type carefully and then press return. You may get a one-time warning to be careful. If you don’t have a login password, you’ll need to set one before you can run the command. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.
The command may take several minutes to run, depending on how many files you have. Wait for a new line ending in a dollar sign ($) to appear, then quit Terminal.
Step 2 (optional)
Take this step only if you have trouble with Step 1, if you prefer not to take it, or if it doesn't solve the problem.
Start up in Recovery mode. When the OS X Utilities screen appears, select
          Utilities ▹ Terminal
from the menu bar. A Terminal window will open. In that window, type this:
resetp
Press the tab key. The partial command you typed will automatically be completed to this:
resetpassword
Press return. A Reset Password window will open. You’re not going to reset a password.
Select your startup volume ("Macintosh HD," unless you gave it a different name) if not already selected.
Select your username from the menu labeled Select the user account if not already selected.
Under Reset Home Directory Permissions and ACLs, click the Reset button.
Select
           ▹ Restart
from the menu bar.