If I choose to exclude living individuals, why are deceased individuals also being excluded?
You have not entered dates in the date of death fields. GED-GEN usually considers an individual deceased if the date of death is not empty. If you do not know when an individual died, specify UNKNOWN before you export your GEDCOM file.
How you do this depends on your genealogy program. Some may use the terms DEAD or DECEASED. If it is another term, you should also run GED-GEN and click the Options button. Then select the Program tab. On the Program tab, select the GEDCOM tab and enter the term your genealogy program uses in place of DEAD or DECEASED.
You can also enable a cut-off year under “Privacy Filters” on the Features tab. Individuals born in or before the cut-off year are considered deceased. This method is less accurate because such individuals may in fact still be living.