I had the same problem with an edit I was working on.
Is the source you're using anamorphic widescreen 1.78:1? If so, you're probably running into the same thing I was. With anamorphic widescreen the black bars aren't burned into the movie. The .vob files have a tag attached to them that lets your dvd player know that it is anamorphic widescreen and it adjusts automatically.
Thing is, as long as that tag is still attatched to the file you should be fine. You can perform a simple test to make sure you're okay. All you need to do is export and render about 30 seconds of footage as an .avi or quicktime file. When you open it the black bars should magically appear on the top and bottom and you will see there is no reason to worry. Make sure check your video in full screen mode to check for the bars.
I don't know much about aspect ratios and such, but someone pointed this out to me when I had this question and I am doing my best to pass on that information. I hope this helps.