"networksetup is trying to modify the system network configuration" dialogue wont go away!
I tried to replicate your environment in a OS X 10.11 VM (including homebrew/cask and rvm). After some trying I have been able to reproduce the error at times.

In my opinion the error is related with wrong permissions in your user folder, a really crappy app (the private-internet-access app) and probably your ruby/rvm environment.

The error you get is (probably) related with SCHelper and nehelper which can't fulfill their tasks successfully.


  File Created: /Library/Preferences/SystemConfiguration/preferences.plist-new
  Modifying Program: SCHelper      Process ID: 773
  Process Owner: System Admin     User ID: 0
  Time recorded: 22:21:04, Sat. Jan. 16, 2016
  ...
  File Renamed: /Library/Preferences/com.apple.networkextension.plist
  Modifying Program: nehelper      Process ID: 183
  Process Owner: System Admin     User ID: 0
  Time recorded: 22:21:04, Sat. Jan. 16, 2016
  ...
  File ownership changed: /Library/Preferences/com.apple.networkextension.plist
  Modifying Program: nehelper      Process ID: 183
  Process Owner: System Admin     User ID: 0
  Time recorded: 22:21:04, Sat. Jan. 16, 2016


Please try the following:


Rename your bash config files:

cd ~/
mv .bash_profile temp.bash_profile
mv .profile temp.profile
mv .bashrc temp.bashrc

Remove all traces of private-internet-access in homebrew:

brew cask uninstall private-internet-access
brew cask uninstall --force private-internet-access
brew cask cleanup
brew cask doctor
brew doctor

Enable your root user, log-out your current user and login as root
Remove the following files and folders:


/Applications/Private Internet Access.app
/Users/your_user/.pia_manager (folder)
/Users/your_user/.pia_manager_crash.log
/Users/your_user/Library/Private Internet Access (folder)
/Users/your_user/Library/LaunchAgents (folder)


I tried to remove all these files and folders with sudo rm ... which wasn't successful. Some files were recreated immediately even after stopping/unloading the respective plist with launchctl. Therefore I used root.
log-out as root, reboot, login as your main user and disable your root user.
Recreate your LaunchAgents folder:

mkdir ~/Library/LaunchAgents

Download, reinstall, setup  and test Private Internet Access
Rename your bash config files:

cd ~/
mv temp.bash_profile .bash_profile
mv temp.profile .profile
mv temp.bashrc .bashrc



I recommend the following:

Follow the instructions and install and use Tunnelblick (instead of installing Private Internet Access).