Not a Pro/E user here...
Have you tried opening the stl in another tool? A lot of folks use Meshlab to repair faulty stl files. If Meshlab can give you more specific information about a problem with the stl you might be better able to troubleshoot. Or maybe it will be able to fix the file for you. I'm not well versed in that either. So far, SF and SFACT have been able to digest everything I've exported from SolidWorks (said to export lousy stl files).
Have you tried exporting other models to compare results? Is the stl file exceptionally large or anything like that?
