You can try the tool at INDDRecovery — a program for restoring corrupted InDesign documents or the blind export to IDML script (in CS6, it won't run in CS3) in the first response to this thread: Adobe Community: InDesign 6 is crashing when attempting to open a particular document. All others are opening OK.
If you want to move this project to CS6, the best advice I can give you is to export each of the component files to .inx from CS3, then open the ,inx files in CS6 and save as new .indd files with new names (DO NOT OVERWRITE the original versions), then add them to a new .indb Book file.
I'm having the same problem when trying to edit CS3 files in CS6. Exporting from CS3 .inx -> CS4 .idml -> CS5 didn't work, Could you please check the application file,
We're just users. like you, so we can't check the application. But I can tell you there is nothing wrong in the code in general for opening files. If your CS3 .inx will not open in CS6 either the files are damaged (do they open in CS3?) or you have a configuration problem like a software conflict on your system with CS6, or the CS6 installation has become damaged (or maybe just the CS6 prefs, so see Replace Your Preferences ).