New Page Sections are all given the same default name of "New Page Section" until you rename them. Connector Xpress treats all sections with the same name as the same object. So, when you save it all of the attributes move to the first "New Page Section" object that you have. To fix this, rename each section before adding attributes to them.
You can rename the sections by double clicking on the header and then filling in the name that you'd like.