There is one document (http://www.geni.com/documents/view?doc_id=6000000017978908009) which has the parents of this James Patrick Calhoun as a Patrick Calhoun, with paternal grandparents of Sir James Calhoun and Mary Falconer.
However, there is a user-submitted family tree on FamilySearch.org which has Alexandar Calhoun and Judith Hamilton has the parents of this James Patrick Calhoun, and paternal grandparents of William Campbell Colquhoun (Calhoun) and Catherine McCausland. (See 'About' for Rev. Alexander Calhoun)
n.b.: There are user-submitted lineages which support both viewpoints on FamilySearch.org.
Any differentiating documentation? (parents of this James Patrick-1688 are currently left with conflict).