In your sample form, you also need to add a rule to QtyBox to update your TotalBox.
Rules run when the field with the rule changes. You set the drop down to C, and at that point QtyBox is blank. So, it has no value to include in your calc. But if you add another rule to the QtyBox field to set the TotalBox field, you'll be find.
As to your new issue - you'll need to filter your data to get the correct value - so, for example, if your drop down uses the SharePoint ID for the value, your formula to set the total needs to include a filter where SharePoint ID from the secondary data source = DropDownBox in the main data source.