I meant a screenshot of your folders; I know that the issue was with building the archive.
EDIT: Actually, considering what you said earlier, I'm going to extrapolate and guess that you took everything inside the patch folder and tossed it in the UFO folder instead of leaving everything be. Because then, there would be no th12.dat in the parent folder so nothing would be extracted, and then trying to build the new dat file later would error on every missing file except the replacement files given, and then it would give you a smaller th12boss.dat file in the parent folder of the UFO folder, which you said happened.
Keep everything in the UFO Boss Rush folder. It should look like this, minus the new files already being there and the work folder.
http://nazr.in/3Qa