The FAMC/FAMS pointer are redundant with the info in FAM groups and therefore many programs including FTM and Ancestry Member Trees’s own GEDCOM import get all the family information from FAM group and thus ignore the redundant FAMC/FAMS pointers without loosing any family information.
Although the GEDCOM works fine in most cases, some programs must rely on the FAMC/FAMS pointers thus causing the problems mentioned.
Therefore we acknowledge this as issue that needs to be fixed to properly output the FAMC/FAMS pointers.
For now the workaround is to import into PAF or FTM, then export again to new file and re-import into your application.

Sorry for the inconvenience…
--Bennett