after trying to encode with BD Rebuilder I get errors. I used my PS3 with Yellowdog 6.1 to transfer the content of the disc over the network. I didnt use any dvd hd to decrypt anything I just went straight to the folder with the BDMV. BD Rebuilder found it and I could see that the movie was there along with the audio.
After it got to 100% is when the error happened. Had something to do with Haali Media splitter. Said something about file not recognized. I guess im going to transfer the blu ray files again from the ps3 over to my computer and try again!