Hi Hugo,
it sounds as if You create that Pop-up widow via the target-attribute in the form-tag, right?
I am no Popup-expert, but I wouldn\'t do it taht way. I would leave the form without the target-attribute.
The new page wich is displaed in the same window after submitting and phping, could let a new window pop up via JavaScript.
The javascript could be something like that:
dummy = open('download.php?id=1234', '', '');
and that code could for example stand in the onload-attribute of the <body>-tag.
Good luck,
Alessandro