That is why I use DVD43. I have never had any issue with it not removing the blockers all the way plus it automatically works in the back ground when you put the DVD into the computer, so while there is a second step in the process you only have to worry about one of them, opening handbrake.
Handbrake does take awhile though (3-5 hours depending on the size of the movie) so I always make sure to set it up before going to bed.
I have been using both or these programs successfully since buying my iPod Video about 5-6 years ago.