A few things I can think of (even though its a little early for me to do any thinking;-) so here goes:
make sure the crossing levels are turned on; the crossing pipes need to be either in the active dgn or in a reference file with their displays turned on; make sure the pipes actually cross in plan view and that you can visualize that crossing in plan view; try running the conflict finder to ascertain whether they're actually crossing; make sure the vertical grid is wide enough to display the crossings; try designing the network or using the Update All Link commands; delete your resource *.rsc files, reboot....
did it work? are there any other specifics about the crossing situation you can share or maybe files for the gurus....