Refer to my other post here:
http://www.e90post.com/forums/showthread.php?t=771408
You probably need a complete overhaul of the programs / files. Don't use the programs you now have to code your car, they will mess things up as the daten files are outdated.
Your INPA will no longer work though once you have followed my procedure. But essentially what you need for coding is NCSExpert (and optionally NCSDummy) only. For me INPA is not something I can't do without.
Good luck!