It's not loading "our page" twice. Please look at other topics on the forum, we've been talking about this recently.
All requests go through index.php, so all your URLs will start with
index.php/, unless you hide it with .htaccess file. The file name after
index.php/ is actual file name which should be displayed, with exception that if it (your main page) is index.php Instant Update will automatically look for and load index-original.php, because it knows it shouldn't load our index.php again.
Sorry if this sounds confusing, it's pretty late and I'm tired, I will explain further if needed.