Magento – How to set quantity of cart as 0 programmatically

This sounds like a similar issue I had about a year ago.

The end result was the same as what you have: totals got doubled by qty (qty * qty)

The problem was tracked down to when customer address got added to the order object, it got added twice as delivery address. Thus the order object had 3 addresses:

• 1 - Billing
• 2 - Shipping
• 3 - shipping (duplicate of #2)

I forget why this happened :( (I seem to recall an observer event doing something funky)

The same happened to the quote object (thus cart)

Since totals calculation hang directly off address objects, totals got doubled by qty.

An easy why to test if you are having the same issue, wipe out the sales_flat_order_address table, and enter checkout. Then check the table for address entries for your order. you should have 2 entries in there.

Additionally, since the issue is related to database entries, once the bug was fixed, it looked like the problem remained/was not fixed. It required removing the duplicates from the database for the problem to resolve for existing quote/order objects.

This happens because the configurable product does not have minimum sale qty and a total qty.
You need to get the simple product that is represented by the configurable product and get the values from it. Try this:

$simpleProduct = null;
foreach ($_item->getQuote()->getAllItems() as $simpleItem){
   if ($simpleItem->getParentId() == $_item->getId()){
       $simpleProduct = $simpleItem->getProduct();
       break;
   }
}
if ($simpleProduct){
   //work your magic with $simpleProduct
}

I didn't test, but it seams like the way to go.
I've tested and this works for me. I was close. Instead of getParentId() it should be getParentItemId(). Here is the code from my checkout/cart/item/default.phtml file:

$simpleProduct = $this->getProduct();
if ($this->getProduct()->getTypeId() == 'configurable') {
    foreach ($_item->getQuote()->getAllItems() as $simpleItem){
        if ($simpleItem->getParentItemId() == $_item->getId()){
            $simpleProduct = $simpleItem->getProduct();
            break;
        }
    }
}
$stockItem = Mage::getModel('cataloginventory/stock_item')->loadByProduct($simpleProduct);
$min_sale_qty = (int)$stockItem->getData('min_sale_qty');
$total_qyt = (int)$stockItem->getQty();

?>
<select name="cart[<?php echo $_item->getId() ?>][qty]">
    <?php for($i = $min_sale_qty; $i <= $total_qyt; $i = $i + $min_sale_qty) : ?>
        <option value="<?php echo $i?>" <?php echo ($i == $this->getQty())? "selected=selected": ""; ?>>
            <?php echo $i?>
        </option>
    <?php endfor;?>
</select>

I'm almost sure that there is an other way of getting the simple product and avoid the foreach loop but this will do for now.