How about a different way of using some of these same tools? Rip to the hard drive using the free section of DVDFab, DVDFab HD Decrypter. You can use this on newer dvds that have more advanced protection that DVDShrink cannot handle on its own. DVDFab HD Decrypter will continue to work even after the trial for the main section expires.
Now, go get a free burning program called ImgBurn. Highly recommended around here, and has replaced Nero for me. www.imgburn.com
Next, go to this rapidshare link: http://rapidshare.com/files/35280436/Shrink_w_ImgBurn.rar
Download the compressed file and extract. You can use 7zip to extract a .rar file if you don't have WinRar. 7zip is free.
Go to C:\ Programs files\Dvd Shrink and drag and drop the new Shrink icon you get out of the compressed file to replace the old one.
This gives you the option in DVDShrink to use ImgBurn automatically when you finish compressing a movie. It takes the place of DVDDecrypter. Once you hit Backup, just look at Select Backup Target and you should now have an option for ISO Image file and burn with ImgBurn. Set it to this and it will keep this option in the future for all your burns.
You should probably set the burning speed in ImgBurn manually, else you will be burning at top speed all the time. I suggest 8x.
And your compatibility problems may have more to do with poor media or too high burning speed than something wrong in Nero 9. You should use Verbatim 16x blank media, or Sony if you can't find Verbatim.