yes you were right it was the flypage. But there is a problem with your mod.

Your mod works only displays the quantity box correctly when the childproduct is a non-downloadable product. As soon as I make it a downloadable prodcut the quantity box has a problem like shown in the pic above. Here is what happens
a) When I select to hide the quantity box it shows the check box at the top left corner.
b) When I select to show it as a standard quantity box it still shows as a check box.