Hi @pjhickman,
Could you provide more information on the coordinate systems you use in the project (GCPs and outputs)?
We had some users contacting us regarding similar issues and the offset you get could be related to the fact that horizontal grid deformation and corrections are not supported in Pix4Dmapper. But I will be able to say more once I got more information on the coordinate systems you use.
More information in the Horizontal grid corrections and transformations post.
Best,