In the recent issue of "The Economist" (Oct 13th 2007) I came across a case demonstrating a cost of use of incompatible versions of softwares. As per the story, One of the delays of the latest Super Jet A380 airplane was the use of two incompatible versions of the computer CAD softwares. (Vertatim from the article ) " The Germans in Hamburg had one system, the French in Toulouse another. When the electrical harnesses came to be fitted in the forward and aft fuseleage sections, many didn't connect with each other. Despite efforts to resolve this, it was decided in Octover last year that only by updating the computer-design tools would Airbus get on top of the problem. That meant a third delay".
This is not a problem specific to the Airbus. This is a often problem not just because of the use of two different softwares, but one software may result into different formats of outputs and often there are losses of information in transforming between the models.