Cannot use VPN after install Charles web proxy

I have the same issue. When I use a proxy.pac file certain applications fail to pick up the settings. Among these are:

• Firefox
• Chrome
• Java apps (like eclipse)

Some apps that do work with the pac file are:

• Safari
• Skype
• Adium
• Evernote

What I have found though, is that when I manually add a proxy server to the system preferences it is picked up by all applications. So something in the pac handling is broken. Maybe old/new APIs in Lion?

You should not use the Web proxy, but to use the Automatic Proxy Configuration, and setup a .pac file. In this file, you specify which domain/hosts you want the proxy.

Check wiki, http://en.wikipedia.org/wiki/Proxy_auto-config, for more information.

A sample may looks like:

function FindProxyForURL(url, host) 
{
  PROXY = "PROXY 127.0.0.1:8000";
  DEFAULT = "DIRECT";

  var domain_list = [
    "blahblahblah.com"
  ];

  for (var i = domain_list.length - 1; i >= 0; i--){
    if (dnsDomainIs(host,domain_list[i])) {return PROXY}
  };
}

The other simple way is to use the Firefox, and install an extension, Autoproxy.