This is because you have not set which isotopes the molecule is.

The 'natural' mass is defined even without that information, but the total exact mass is different for 12C or 13C, etc...

What you can do instead is:

mfManip = MolecularFormulaManipulator
mf = mfManip.getMolecularFormula(mol)
exactMass = mfManip.getMajorIsotopeMass(mf)

(Added pointers to the JavaDoc, r14370).