I'm not quite clear what problem is remaining. If you had set Import orders with status: to "Any", and had Update Status set to "Yes," then it indeed would do what you described. Most people don't change the status to Shipped until the orders are imported into QB, and they process the order and do shipping after it is in QB. If you do all your order processing in Zen Cart and just import the orders into QB to update your accounting, then you probably should uncheck "Update Status" so QBI doesn't affect it.
Thanks,
Adam
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