We had the problem, that we have a short list of countries we ship to:

But the country list for the invoice and shipping address in the checkout is complete.

Config

The configuration is fine as you can see above. I checked the cache, because I thought it might be wrong - but the config cache too was fine.

Cache

Digging into the issue shows, that more caches are involved:

\Mage_Checkout_Block_Onepage_Abstract::getCountryOptions
public function getCountryOptions()
{
    $options    = false;
    $useCache   = Mage::app()->useCache('config');
    if ($useCache) {
        $cacheId    = 'DIRECTORY_COUNTRY_SELECT_STORE_' . Mage::app()->getStore()->getCode();
        $cacheTags  = array('config');
        if ($optionsCache = Mage::app()->loadCache($cacheId)) {
            $options = unserialize($optionsCache);
        }
    }

    if ($options == false) {
        $options = $this->getCountryCollection()->toOptionArray();
        if ($useCache) {
            Mage::app()->saveCache(serialize($options), $cacheId, $cacheTags);
        }
    }
    return $options;
}

So I checked the cache entries for DIRECTORY_COUNTRY_SELECT_STORE_DE and found a complete list of countries. So the assumption is: Something "poisons" the cache.

So, what is writing into this cache and maybe we have a broken extension - we don't.

\Mage_XmlConnect_Model_Simplexml_Form_Element_CountryListSelect::_getCountryOptions
\Mage_XmlConnect_Block_Checkout_Address_Form::_getCountryOptions
\Mage_Directory_Block_Data::getCountryHtmlSelect
\Mage_Checkout_Block_Onepage_Abstract::getCountryOptions
\Mage_Catalog_Model_Product_Attribute_Source_Countryofmanufacture::getAllOptions

If we look further into it, we can assume the problem is not from here:

\Mage_XmlConnect_Block_Checkout_Address_Form::_getCountryOptions
\Mage_XmlConnect_Model_Simplexml_Form_Element_CountryListSelect::_getCountryOptions
\Mage_Checkout_Block_Onepage_Abstract::getCountryOptions
\Mage_Directory_Block_Data::getCountryHtmlSelect

because all of them filter the country list via Mage::getModel('directory/country')->getResourceCollection()->loadByStore();, therefore the filter of the config is applied.

\Mage_Catalog_Model_Product_Attribute_Source_Countryofmanufacture

The source model doesn't do correct filtering.

How is the cache filled with wrong data?

This is the tricky part. The only place were I know the source model is used is the backend. But Mage::app()->getStore()->getCode() is always admin. Even when you edit data for another store view.

After digging a while I found out, that when I place a configurable product into the cart one of our extensions reads the country of manufacturer in the frontend and poisons the cache.

I fixed the problem with a rewrite:

class Project_Bugfix_Model_Catalog_Product_Attribute_Source_Countryofmanufacture
    extends Mage_Catalog_Model_Product_Attribute_Source_Countryofmanufacture
{
    /**
     * Get list of all available countries
     *
     * @return mixed
     */
    public function getAllOptions()
    {
        $cacheKey = 'DIRECTORY_COUNTRY_SELECT_STORE_' . Mage::app()->getStore()->getCode();
        if (Mage::app()->useCache('config') && $cache = Mage::app()->loadCache($cacheKey)) {
            $options = unserialize($cache);
        } else {
            if (Mage::app()->getStore()->isAdmin()) {
                $collection = Mage::getModel('directory/country')->getResourceCollection();
            } else {
                $collection = Mage::getModel('directory/country')->getResourceCollection()->loadByStore();
            }
            $options = $collection->toOptionArray();

            if (Mage::app()->useCache('config')) {
                Mage::app()->saveCache(serialize($options), $cacheKey, ['config']);
            }
        }
        return $options;
    }   
}