Six or seven years ago (?) I built a crossover Module (see photos in the Crossover Module album for this group) and encountered the same issue. The solution for me was to build a balloon end module with special wiring. You could also build a non-end module with special wiring. We discovered (painfully for Brian K and others) that you cannot insert a normally wired module between the two.
Good luck on your crossover module, and they provide great train views.
Check out my photo album and also the two part series in Z Track magazine from a few years ago where I described in detail the building process. You'll need a 6 foot module or longer to maintain 2 degree or less gradients, with one set of tracks dipping down under the elevated other sets of tracks.