Wifi instance on save()

That's an odd one - just tried here with:

var WIFI_NAME = "...";
var WIFI_OPTIONS = { password : "..." };

var wifi;

function getPage() {
  require("http").get("http://www.pur3.co.uk/hello.txt", function(res) {
    res.on('data', function(d) {
      console.log("--->"+d);
    });
  });
}

function onInit() {
  wifi = require("Wifi");
  wifi.connect(WIFI_NAME, WIFI_OPTIONS, function(err) {
    if (err) {
      console.log("Connection error: "+err);
      return;
    }
    console.log("Connected!");
    getPage();
  });
}

then:

Upload...
>save()
=undefined
Compacting Flash...
Calculating Size...
Writing..
Compressed 114368 bytes to 4481
Running onInit()...
Connected!
--->Hello World!
>save()
=undefined
Compacting Flash...
Calculating Size...
Writing..
Compressed 114368 bytes to 8578
Running onInit()...
Connected!
--->Hello World!
> 

And it seems to work...

Could it be that in setConfig you're actually forcing a connect again, then saving?

In that case, it'd be saving the current state (which is in the middle of a connection), but then onInit is firing off a second connection?

Having said all that, saving the network details the way you're doing (re-saving all your code) isn't ideal. In 1v96 I added Storage module which allows you to save small amounts of data. For instance:

// update wifi details
function setConfig(name, password) {
  require("Storage").write("wifi",{
    name:name, password:password});
}

function onInit() {
  var WIFI_NAME = "...";
  var WIFI_OPTIONS = { password : ".." };
  var wifiConfig = require("Storage").readJSON("wifi");
  if (wifiConfig) {
    WIFI_NAME = wifiConfig.name;
    WIFI_OPTIONS = { password : wifiConfig.password };
  }
  console.log(WIFI_NAME,WIFI_OPTIONS);
  wifi.connect(WIFI_NAME, WIFI_OPTIONS, function(err) {
    ....
  });
}

So now when you change your wifi details it modifies just the wifi details in a file called wifi, but leaves everything else the same (and doesn't require a reboot).