i've seen a similar problem in an idw, my suggestions going to be a little strange, and you may not be able to do it.
open the assembly in inventor 7, then save it, then go open the idw in inventor 6. i was seeing a problem like that with one of our customers files. i'd open the drawing in six, and immediatly crash, i could open the drawing in seven, but couldn't always save it. If i opened the assembly in inv. 6 i'd get all sorts of warnings, constraint problems, etc. if i opend the assembly in inv. 7, the assembly would ask to update before opening, i'd let it, and then just save it.
as i said, it's a bit of a weird fix, and won't be practical if you don't have inventor 7