After doing all sort of tests during the last two days I got it figured out how it works.
It HAS something to do with .paa textures combined with another one that has transparency.
Every .paa textured face that has a higher index than the transparent one is invisible behind it, the ones that have a lower index are shown.
The thing that took me so long to figure this out is that you need a named selection in O2 to let Buldozer show this effect.
If you don't have any named selection all faces behind a transparent texture are shown in Buldozer no matter what index they have. It doesn't have to be a special named selection, just one that is shown in the named selection window. It's sufficent to let O2 show the components by using the "Find Components" command, you don't have to create one.
Faces that are textured with .pac files are not effected by this, they are allways shown behind a transparent texture.
Now don't tell me that nobody in here knew this allready Â