Could you uplaod the model or part of the model to have a look?
What version of Revit are you using?
Are the structural column and structural framing familes ones that have been created by Autodesk or ones someone else has created?
If created by someone else they must be setup exactly as the following link to work with structural connections - https://help.autodesk.com/view/RVT/2023/ENU/?guid=GUID-6244E741-5D14-4DAD-AE25-5069F71B69F3
Rob Merriman, AEC Technical Lead, Graitec
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At a first glance I would say the connection is not meant for use with rectangular hollow sections. Try whether it works if you exchange one of the columns for a more standard H beam. If that works, generate a variant of the hollow section that looks hollow but is cut open at one corner. That way it will look alright in plans but boqs will be a bit off. Good luck.