We investigate a recently proposed method [J. Chem. Phys. 108, 9206 (1998)] to obtain tunneling splittings from short time cross-correlation matrices that were propagated according to the semiclassical propagator of Herman and Kluk. The energy levels were extracted by harmonic inversion of the cross-correlation matrix using the filter diagonalization technique. The aim of this study is twofold: First, the short time behavior of the Herman-Kluk-propagator and the meaning of using cross-correlation matrices rather than autocorrelation functions is addressed. Numerical examples are given for one- and two-dimensional model potentials. Second, the performance of the method is investigated for a system with considerable anharmonicity and coupling. Here the proton transfer in 3,7-dichlorotropolone is considered using an ab initio reaction surface Hamiltonian approach. For this example also the extension to more dimensions is critically discussed. (C) 2004 American Institute of Physics.