We study the Bloch-Messiah reduction of parametric down-conversion of light in the pulsed regime with a nondegenerate phase matching providing generation of twin beams. We find that in this case every squeezing eigenvalue has multiplicity at least two. We discuss the problem of ambiguity in the definition of the squeezing eigenmodes in this case and develop two approaches to unique determination of the latter. First, we show that the modal functions of the squeezing eigenmodes can be tailored from the Schmidt modes of the signal and idler beams. Alternatively, they can be found as a solution of an eigenvalue problem for an associated Hermitian squeezing matrix. We illustrate the developed theory by an example of frequency nondegenerate collinear twin beams generated in beta barium borate crystal. In this example we demonstrate how the squeezing eigenmodes can be approximated analytically on the basis of the Mehler's formula, extended to complex kernels. We show how the multiplicity of the eigenvalues and the structure of the eigenmodes are changed when the phase matching approaches the degeneracy in frequency.