It could be that you have two versions of MW3, one on Steam and one cracked. The thing is that ChromatiX installer imports only to one location at a time, while no custom folder can be selected if you have Steam version. This is sort of an intentional bug. However, you could download TextureHackOnly.zip and extract its contents somewhere on file system. After extracting you can open appropriate .iwd archives in 'MW3/main' folder and add iwi files (texture hack). It may take a bit longer but it will surely work.
Also for anyone else struggling with this type of problem, installer source is available and you could easly change few parameters and even post it here.