Puerto - It's hard to diagnose your issue from a distance but I suspect what you need to do is start over with the import process.
I tried to duplicate your situation by installing a fresh copy of OSX on a clean hard drive, which includes the iTunes application. I also attached another external hard drive to represent the one you want to have as your music repository.
I then booted up the computer from the external hard drive with nothing but the fresh operating system on it, opened iTunes and went through the process I described above to put the iTunes music library on the second hard drive.
I inserted a CD, dragged the music files on it into the open iTunes window on the boot hard drive, waited while they were copied and then checked their location. They were copied to the second hard drive, the one I had chosen via the iTunes preferences. Playing them from iTunes on the boot drive worked perfectly.
I tried to duplicate your situation by installing a fresh copy of OSX on a clean hard drive, which includes the iTunes application. I also attached another external hard drive to represent the one you want to have as your music repository.
I then booted up the computer from the external hard drive with nothing but the fresh operating system on it, opened iTunes and went through the process I described above to put the iTunes music library on the second hard drive.
I inserted a CD, dragged the music files on it into the open iTunes window on the boot hard drive, waited while they were copied and then checked their location. They were copied to the second hard drive, the one I had chosen via the iTunes preferences. Playing them from iTunes on the boot drive worked perfectly.