Poor handling of modification states when exporting to SBGN-ML

Example is inflamation signaling (inflamation_cd.xml) which when converted to SBN-ML results in this file. When this is then exported to a graphics format or imported to Newt, it results in too big rectangles representing modification states and shifted circles for species modification states are off. However, when the original cd file is uploaded to Newt directly, everything looks correct.