It looks like the canvas gets resized for some reason. In yEd we introduced some shapes in top-left and bottom-right corners as a way to have fit coordinates to the intended background image. Exported from yEd PNG looks as it supposed to be, with those shapes in two corners. Then, in SBGN and CellDesigner, there is an additional space on the right and on the left.
It looks like the canvas gets resized for some reason. In yEd we introduced some shapes in top-left and bottom-right corners as a way to have fit coordinates to the intended background image. Exported from yEd PNG looks as it supposed to be, with those shapes in two corners. Then, in SBGN and CellDesigner, there is an additional space on the right and on the left.