  We show that the topological string partition function with D-branes on a
compact Calabi-Yau manifold has new anomalies that spoil the recursive
structure of the holomorphic anomaly equation and introduce dependence on wrong
moduli (such as complex structure moduli in the A-model), unless the disk
one-point functions vanish. This provides a microscopic explanation for the
recent result of Walcher in arXiv:0712.2775 on counting of BPS states in
M-theory using the topological string partition function. The relevance of
vanishing disk one-point functions to large $N$ duality for compact Calabi-Yau
manifolds is noted.
