Hi
Are you saying that the Circle/Rectangle/Position controls....Like this...are also appearing with your exported project?......

If your are seeing this happen then there is a problem.
However, it is normal for them to appear in the project itself during editing. The Scale/Rotation/Position controls appear on the Preview Screens as shown above of overlay clips and images. Being overlays I think NCH see this as a quick way of adjusting the images so they will fit where required over any clip on a lower track without having to invoke the FX for the selected clips.
They should not export though and also not be seen in copied clips.
Nat