I'm not sure if this is the right place to post a bug report, but I've noticed the following problem:
When using DVD to DVD and a mode where you can select the default audio stream (only tried with Full Movie and Customize - menus removed). The disc stream number is used, and not the "result" stream number. E.g. I select stream number 3 out of 4. At the same time I want to remove stream 2. The result in this case is that the default stream is 3, but this is now the original stream 4.
The same applies when I use DVDFab to remove content from discs ripped with DVD Shrink. DVD Shrink don't remove audio streams like DVDFab, but leaves "dead" streams. These streams does not show up in the DVDFab user interface, but I see them when playing with e.g. WMP.
My workaround is to use pgcEdit to change the stream, but this should be easy to fix in DVDFab.
I've noticed this problem with the 3 latest versions (only been using DVDFab since mid December)