Hmm. I've tried a number of different options - the only difference I saw was that character set ANSII supported accents - but I suspect that I could upload the same GEDCOM that doesn't work on FamilyTreeDNA to WorldConnect and WC could handle it. I seem to recall WC dealt with the preferred facts correctly. So maybe the question really should go to FamilyTreeDNA, wrt why it's ignoring the preferred values? The GEDCOM 5.5 format has to be supporting the preferred value flag or indicator, if WorldConnect can see it.
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