Johnhayesvfx
In case anyone stumbles onto this thread, I had this issue also. What fixed it was adding a clean node with remove attributes after the object merge node (or what ever node is bringing in the mesh box object from unreal into Houdini.) Unreal is passing some data from the box into Houdini that does some thing odd to the orients of the boxes, regardless if you set them up in the correct angles / pivots with the building utility node.
This method worked for me. I also used a "labs dissolve flat edges" node after the clean node.
I am on Houdini version 20.5.613, and unreal version 5.4.4.
Thank you for the suggestion!