I found that by using the above that Apache was being talked to by the Ipad/Iphone – The post by Kyle2011 at https://discussions.apple.com/thread/3089948?start=0&tstart=0 filled in the rest of the solution.
Basically at the bottom of the retrieve.php page you need to redirect the browser to a directory by using a line similar to the following:-
header("Location: https://www.example.com/enrolment?params={$params}");
Where enrolment is a directory – this then calls the DirectoryIndex (typically index.php) which can then display stuff to your user.
To populate the $params variable you need the following line at the top of your retrieve.php script
$data = file_get_contents('php://input');
You can then parse the $data string to get what you need (try file_put_contents("data.txt", $data); or Kyle2011’s example)
I also changed the Payload UDID to something different by using udidgen in a terminal on a Mac rather than just using whatismyudid.com’s.
Update: From iOS 7.1 some of the files (the .plist IIRC) need to be served over https:// – they will fail to install if everything is served over http:// – probably best to serve everything including the .ipa over https:// to ensure future changes on Apple’s side don’t cause a problem.