Missing Download PDF Button in Orders for Craft Commerce
The Download PDF button will show if the OrderModel that gets passed to the template's getPdfUrl() method returns a URL.

You can see the logic it uses in commerce/models/Commerce_OrderModel.php, function getPdfUrl().

It gets the orderPdfPath Commerce setting, then checks if that template exists on the front-end templates folder.

My guess is you've got something messed up with the path to that template somewhere.