So when k = 19, sage.interfaces.latte.count <http://doc.sagemath.org/html/en/reference/interfaces/sage/interfaces/latte.html> and P.integral_points_count() give different answers. This seems to be the cause of the difference. Here is some more code showing the difference.
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from sage.all import Polyhedron from sage.interfaces.latte import count eqns = [ [0, -1, 0, 0, 0, 0, -1, 1, 1, 0, 0, 0, 0], [0, 0, 0, 0, 0, -1, 0, 0, 1, 1, -1, 0, 0], [0, 0, 0, 0, -1, 0, -1, 1, 0, 1, 0, 0, 0], [0, 0, 0, -1, 0, 0, 0, 0, 0, 0, 1, 1, -1], [0, 0, -1, -1, 0, 1, 0, 0, 0, 0, 0, 1, 0], [0, -1, 1, 0, -1, 0, 0, 0, 0, 0, 0, 0, 1], [-100, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1], [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0], [-19, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] ] ieqs = [ [-1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [-1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], [-1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0], [-1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0], [-1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0], [-1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0], [-1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0], [-1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0], [-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0], [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0], [-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1] ] P = Polyhedron(eqns=eqns, ieqs=ieqs) print(P.integral_points_count()) print(count(P.cdd_Hrepresentation(), cdd=True))