I just imported (again) my tree from the old FamilyTreeMaker, and found my great grandmother's with her parents link were broken. I don't know how extensive it is.
I don't think this is a PhpGedView problem. In all likelihod, your Family Tree Maker database is screwed up, causing it to export to a GEDCOM incorrectly.
You need to look at the GEDCOM (using a plain text editor) to verify that your grandmother is listed as a FAMC in her parent's family.