The command line switches (-wsLoad_InRoads_SS2/SS3) should prevent the wrong version of the cfg from loading.
If it is not the workspace, I would then suspect that there are some InRoads SS3 objects (corridors, civil geometry, survey data, civil cell, etc..) in the DGN file they are opening. Do they get the error with only certain DGN files? Can they test opening InRoads SS2 in a SS2 workspace with a new DGN file?