Something is wrong - PICO

When I send my code to the PICO by calling save() in the WebIDE, everything appears to work. I then unplug the USB cable, then when I either plug the USB cable back in or connect a power source/battery, it is obvious that the PIC is not running the code I just sent it. In some cases it seems to run a previous version that I sent to it via this method, in other cases it just seems to do nothing.

No errors are reported via the WebIDE console, everything appears to be working, but it clearly is not. This happens on 2 different PICO's and both with the previous and latest firmware. Also tried on both Windows and OSX, same results.

Seriously WTF is going on here, what am I missing? So frustrating...

As an example, this is how simple the code is that I'm testing it with right now.

function blah(){
  setTimeout(function(){
    digitalWrite(LED1, 1);
    setTimeout(function(){
      digitalWrite(LED2, 1);
      setTimeout(function(){
        digitalWrite(LED1, 0);
        digitalWrite(LED2, 0);
      }, 1000);
    }, 1000);
  }, 1000);
}

blah();