Silly me, it seems I was adding the products to the quote the wrong way. This is the way it works now:
$quoteItem = Mage::getModel('sales/quote_item');
$quoteItem->setProduct($productObj);
$quoteItem->setPrice($productObj->getPrice());
$quoteItem->setQty($singleProduct->quantity);
$quoteItem->setQuote($quoteObj);
$quoteObj->addItem($quoteItem);