Listing the payment and shipment methods (as far as know) is also buggy in original Virtuemart as well. John's screenshot is just the proof.
Actually there is no logical way that our VM Template might corrupt this sorting order. Templates are not responsible to list or order anything. (including the sorting in category browse page).
Templates (in general) have this PHP lines to print DATA (this can be a list of products in category browse page, or a list of payment methods in the checkout page, the idea is always the same);
foreach ($somethinglist as $something) {
echo $something;
}
As you see in this lines above, there is nothing about the "sorting".
The sorting the DATA involves only when the PHP is connected to MySQL, and templates never connect to MySQL.
Virtuemart is taking care of these arrangement of data in a prescribed sequences (Either based on ascending or descending of ID or what ever parameter is chosen in back-end for default sorting) with the files in this folder: /administrator/components/com_virtuemart and our template has nothing to do with this folder.
Regards.
Support & Development.