Quantum systems with discrete symmetries can usually be desymmetrized, but this strategy fails when considering transport in open systems with a symmetry that maps different openings onto each other. We investigate the joint probability density of transmission eigenvalues for such systems in random-matrix theory. In the orthogonal symmetry class we show that the eigenvalue statistics manifests level repulsion only between every second transmission eigenvalue. This finds its natural statistical interpretation as a staggered superposition of two eigenvalue sequences. For a large number of channels, the statistics for a system with a lead-transposing symmetry approaches that of a superposition of two uncorrelated sets of eigenvalues as in systems with a lead-preserving symmetry (which can be desymmetrized). These predictions are confirmed by numerical computations of the transmission-eigenvalue spacing distribution for quantum billiards and for the open kicked rotator.