There's an updated version for important bugfixes, so check it out.

I have not experienced this digital blocks showing from what you described. I used to do this with episodic disks where there are similar intros and endings in the same VTS.

Do you see this digital block in software player? Is this like a glitch?

Not sure if this relates to Open/Closed GOPs or missing some info from removed navpacks.

Maybe Dimad would want to take a look at this trouble before-and-after clip as this deals with vob cutting. Let's wait for his input.