It could be your throw out bearing. It may be worn, but if your clutch is engaging fine, and all. I don't know how it could be the throw out bearing at that point.
I had a similar problem like yours; but it was not related to my clutch, and I heard no weird noises using my clutch. It turned out to be my wheel bearing. I doubt that is your problem either.
Try to idle the car for 15 mins, and see if the noise comes back, and have you head in the engine bay to see if perhaps you can locate exactly where the noise is coming from.
Sorry not being much help here........