This sounds alot like the problem I was having with my VT when I first got it... On cold starts..clutch in..engine on...in neutral...clutch out... then I would start hearing what is best described as a couple of small ball bearings being rolled and shaken around in a tin can...I didn't have any issues for about 1100 miles, then it started to shift hard through all gears, not want to go in reverse, not want to go into 1st period... so after getting my dealership to admit that they heard the noise and replicated the shifting issues, they replaced the throw-out bearing... well after only driving for 5 minutes I could tell that was not the issue, and it was acting the same... so back to the dealership I go the next day. They let the car sit over the weekend and monday morning sure enough they can hear the noise again... so Hyundai tells them to pull the entire transmission and they sent a replacement. I have about 6000 miles on the "new" 6speed and haven't had another issue, no noise on cold starts and no shifting issues. If I were you Chippy I would get it looked at again, if the input shaft bearing is bad and fails you will have a nice mess on your hands. GooD LucK!!!