I think the issue you are talking about was the Invalid Reference to an Audio Stream? (which is created during the DVD Build mode out of DVD Architect).
Using the DVD Architect 4 Trial Download, it appears the issue is still there...
"The issue is going to be addressed in the first update that comes out for DVD Architect (4), not the initial release."
As to DVDA1, DVDA2, or DVDA3 I don't think there are any plans to address this problem at this time. Which is not., for me, a positive state of affairs and points to Sony being more concerned with the new release than fixing the old one.