Well, if this is the only item category / order type where this happens then wouldn't it be reasonable to suspect some kind of custom code is involved?
In this case since even the order type description is not standard who knows what else could have been modified in your system? In general, I feel it's not a good idea to modify standard types. If there is a need to make changes, create a custom type. In this case if anything goes wrong at least you'll be able to do a quick test with everything standard to find whether it's how SAP works in general or not.
Also if the standard configuration was preserved then you would've had a reason to contact SAP support and ask them why the same process works differently for different item categories. From the technical standpoint, I don't see any requirement to combine the lines and, as you said, they're not combined in a regular 3rd party process. This would be a rather strange design.
We don't use consignment, so I can't check in our system. But my money would be on a bug or some user exit in your system. There is transaction ANST that can help with research.
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