Sorry for the "bounce", but I re-read my old post and realised that I had not been real clear on my problem.
The game has stopped using the "Ships2.dds" file. I put the game on my laptop to see if I could replicate the problem. I also did not use the Ships2.dds file update that I had created on my laptop, just to maintain a "control" environment. I had to play about 15 or 20 games, but eventually it did it there as well.
What I keep getting is a game with 4 ship models instead of the full 8. When the problem first happens, I changed the file names of "Ships.dds" and "Ships2.dds". This works, but only swaps which 4 ship models the game uses. Any ideas on how to fix this? I can only get my game to view 4 of the ship models at a time.