Typically I change the sequence dimensions in the settings after I am done editing. Reason being that sometimes clients want a few different, very specific aspect ratios for output.
For some reason this time around, any of my clips with a motion fx applied, the motion is not translating proportionately. All of the clips with no fx are adjusted proportionally, but the one with fx... their relation to the position of the project are not.
For example an item that was centered is now in the right corner.