What is your procedure? You should be doing this:
1) Open disc in DVDShrink (or ripped files from DVDDecrypter, ALL files, repeat ALL files, ripped in "File Mode", not "IFO Mode".)
2) Hit "Reauthor".
3) Drag the main movie title from the right pane to the left. Usually the main movie titleset is "Title 1".
4) On the "Compression Settings" tab, get rid of any unwanted audio and subpicture streams.
5) If that's all you want to do, leave compression at "Automatic". If you wish to afterwards re-encode the movie with DVDRebuilder, for example, select "No Compression".
6) Hit "Backup". You will retain all chapter info with the main movie only.
Is that what you're doing?