You might try cleaning the electrical contacts. If there is a bad connection or no connection then the Speedlight assumes the camera is not a CLS camera.
The pre-D90 dSLRs do not have full control of the SB-400, but that does not mean a different CLS. The SB-600/800 still works as CLS uints on the newer dSLRs. The other change is that the SB-400/700/900/910 do not work with TTL film cameras but the SB-600/800 both support TTL film cameras. I would not consider that a different CLS.