I haven't even changed those. I need to get the originals again.
Ignore me, I know what happened. When I was applying the new files, I copied all of Cyrem's rips, including the particle effects, into the TESt folder, hence they broke. Now I know what he means by "Transparency still needs work".
Cyrem's rips have the colors off very slightly (and I'm not sure why, I'm tempted to blame the LR1 game engine for supplying funky data to the graphics card).
The TDB files (texture listings) specify a transparent color for some textures.
It's simply that the TDB (and the original bitmap's palette) specifies the grass transparent color as RGB(5,42,23) while Cyrem's ripped texture has RGB(0,41,24) as the background color.