I now have a working catapult on Independence, Belleau Wood and Bataan. In DBW\USN Light Carriers\3do\ships\USSBataanCVL29_1944\ there is a \ShortDeck and a \StandardDeck directory. Both contain the file Hull2.msh. Both files were created on 20 July 2008, but at different times. The ShortDeck version was created at 1:41 AM and the StandardDeck version at 7:09 AM. I found that the ships with working catapults had a copy of Hull2.msh in the ship's name directory, e.g. USSCowpensCVL25_1944, that was created at 1:41 AM and the ships that did not have a working catapult had the 7:09 AM version in that directory. So, I copied the 1:41 AM version into the Independence, Belleau Wood and Bataan directories, overwriting the newer file, and now those ships have working catapults.
Cheers,
Riptide