make sure you CD1 and CD2 suffixes have a dot in front of them:
e.g. Titanic (1997).CD1.avi and Titanic (1997).CD2.avi
If your movies are named this way, Media Companion will not provide two NFOs for each movie - BUT it will name the NFO and TBN as Titanic (1997).CD1.nfo, etc.
That is, it will ignore the CD2 file (which is good, so there's no duplication) - but it will actually use the CD1 in the name for whatever it generates.
You will have to manually remove the CD1 from the filenames. You can automate this very easily by using a program such as Bulk Rename Utility (google for it, it's free). Very easy to use - just point to the folder you want (for all your movies), hit the recursive button (so it searches subfolders within your movies folder), and type .CD1 in the remove box.
There was an announcement that the next couple of versions should address this issue, so that manual renaming won't be necessary.