New-Bee ... My biggest Espruino fear is coming true!

Ok, this will be fixed in the next update of the Web IDE that I do (or you can grab the latest from GitHub if you can't wait ). For now, just change your code to:

digitalWrite([LED1,LED2,LED3],4);
setTimeout("digitalWrite([LED1,LED2,LED3],2);", 1000);
setTimeout("digitalWrite([LED1,LED2,LED3],1);", 2000);
setTimeout("digitalWrite([LED1,LED2,LED3],0);", 3000);