Maybe the 5 seconds between may not quite be enough for the cameras long exposure noise reduction ?
When I first got a D5000 i took 250 shots of the clouds but it was 1/250 sec and 1 second interval, that worked ok, but I did forget to turn off the lens VR function, so the images jumped around a lot.
afraid I can't test it now, d5000's gone walkabout with eldest son !