This is a really simple thing...
Never, under any circumstances, copy a shader file directly from JK2 to JK3 and leave it with the same name!
To expand on that, JK2 has a shader file called bespin.shader; JK3 also has a file called bespin.shader but it is different to JK2's ( it has new textures and removes some old ones). The Matrix Reloaded map has copied bespin.shader directly from JK2 and left it in the PK3 with the same name. The result? The game no longer loads the new bespin.shader file meaning if you play any bespin maps or maps that use JK3's bespin textures you'll see the grey and white grid.
It isn't just the Matrix map, others have been doing this too and it has to stop! If you can't be bothered to fish thru the JK2 shader file for the shaders you used, at least rename it to jk2bespin.shader.
can someone make this a sticky!