If you rip the disc with the plugin, after ripping the files are cleaned from the all the crap inserted by protections. This method should allow you to get rid of the error in dvd shrink.
You can also do the cleaning step on the files you have, using fixvts manually. I suggested the plugin method because is fully automatic, and require only a minimal interventions.
Read the guide I posted previously: it contain all informations on the cleaning process to render ripped files complaining with dvd shrink