If you install the full installation package of The Word (3.1.2.1027 - 15 Mar 2010) and then install the latest NET Bible (Limited notes edition, 13 Apr 2010) you will get two commentary notes files in the Books folder. One is named "netnotes.cmt.twm" which was installed with the full package installation of The Word and the other is named "NET Bible's notes.cmt.twm" which was installed with the latest NET Bible (limited edition) addon. Perhaps the latest NET Bible (limited edition) needs to be updated in the full installation package so that there is only one set of commentary notes for the NET Bible in the Books folder.
Thanks again for such a great program. May the Lord continue to guide and bless this labor of the Lord for His blessed glory.
Jim