Hi Dennis,
I would give these explicit Pin Numbers (e.g. 1, 2, 3, 4, 5, 6) in Cell Editor rather than alpha characters. By specifying the Pin Numbers as 'A' and 'C' you are not giving the tool information as to what should be the first pin. In other words, I'd have the cell look like this:
You can then short those pins in the schematic, or by defining a Signal or Supply Name within the part's Pin Mapping:
There is a way to set Pin #1 within the ODB++ data through Valor NPI - within Graphic Station you can navigate to Component > Set Pin #1. I've attached a screenshot of that below:
However, I'm hesitant to recommend that because you're fixing the generated data rather than the underlying cause (the faulty cell).