Why not read my earlier replies on this subject?
Did you pre-process the movie? Any pre-stream processing?
DVD2one likes the files as unaltered(raw) as possible?
The prediction is based on information in the IFO and not the actuall file itself. If you preprocess the data, the IFO's aren't corrected so DVD2one estimates the size based on information that's isn't there anymore.
Sometimes the size is just a mather of trial and error. This is something that's going to be changed in the future, but as explained before a quite drastically change in the entire engine.