Ok, thanks for the description of what was done on this page. I looked at the line of code that should be updated in the store order details server behavior and it did not seem fully correct to me so I updated it. I went to line 1171 and updated it to be like this:
$WA_fieldValuesStr = WA_eCDB_ConvertNumber("".$_SESSION['OrderID'] ."") . "|" . WA_eCDB_ConvertNumber("".$WA_Store_Cart->DisplayInfo("ID") ."") . "|" . "".$WA_Store_Cart->DisplayInfo("Name").(((strpos($WA_Store_Cart->DisplayInfo("Description"), "--")) !== false)?strip_tags(substr(nl2br($WA_Store_Cart->DisplayInfo("Description")),strpos($WA_Store_Cart->DisplayInfo("Description"),"--"))):"") ."" . "|" . WA_eCDB_ConvertNumber("".$WA_Store_Cart->DisplayInfo("Price") ."") . "|" . "".$WA_Store_Cart->DisplayInfo("SKU") ."" . "|" . WA_eCDB_ConvertNumber("".$WA_Store_Cart->DisplayInfo("Quantity") ."") . "|" . WA_eCDB_ConvertNumber("".$WA_Store_Cart->TotalColumn("DiscountApplied") ."");
I'm including the updated version of this page for you as well. Please give this a try to see if it resolves the issues you are experiencing with the query and the product options.