Best thing to do before waltzing off to the dealer is re-check the clutch adjustment. Make sure that the cable is adjusted correctly at the gearbox end, it's hard to describe in print, but here goes.
Loosen the cable from the lever end, by screwing the brass fitting all the way in to the lever perch. Then go to the gearbox end and check how much play there is in the actuating lever. It should be about 1-2 mm. By this I mean, grab the actuating lever with your finger, push it, and see how far it moves towards the direction of pull of the cable before it stops. If it's not 1-2 mm, then adjust it by loosening the lock nuts either side of the cable carrier, then tighten the one closest to the cable until you get the right freeplay. Once this is right, then go up to the lever perch and screw the brass fitting out until you have about 2-3mm of play at between the lever and the perch itself.
Then start the bike, put it in 1st - ignore any clunks, but see how far out you have to release the lever before the clutch starts to move the bike. It should be somewhere between 1-3 CM (an inch or so). If it's less, then you have too much free play still. If it's more, then not enough free play.
The S3 boxes are very clunky when new and do settle down, but from the sound of what you are saying, the clutch is improperly adjusted, which is a simple check and re-adjust that any one can do.
Hope this helps,
Mick