baber2, you are just doing something wrong and do not understand the software. The entire point of DVDshrink, CloneDVD, Recode, DVD2One, etc. is to transcode (shrink) an entire DVD9 down to fit on a DVD5 disc, extras and all.
It sounds like you just removed some of the features (extras) and got it to work. Suggest you read up on the guides around and practice. It will come.