Well, it sounds as if you have tried all the suggestions I would have for the issue. The cross section sets should be recognized even if the InRoads data is not loaded but we do recommend you have ALL the .alg and .dtm files loaded in the program which were used to create the sections.
You also mentioned trying the graphics Translator which I would suggest as well. This usually only helps when bringing data from a prior version (i.e. InRoads 2004 Edition), but we try it just to make sure.
What is the exact version of InRoads SS2 you are using? Perhaps a reinstall or an update to the latest release (08.11.07.615) could help.