I recently bought a manual 2014 VF SS storm and am also having problems with the gearbox.
At times if I release the clutch I get thuds and clunks. I can sit there not moving and it will make this noise by just pressing and releasing the clutch. It doesn't always do it tho.
It also at times engages differently than it did last shift. EG, it will make a clunk going from 1 gear to the next (upon releasing the clutch and no matter if I do a slow slip release or a faster one). Next time I do the same change from the next set of lights there is no noise at all, and it seems like a perfect shift..... it just seems weird.
It does however seem to shift nice when your somewhat into it, however thats not practical for driving to work everyday.......
I should mention this is my first holden, tho I've never experienced this from any other gearbox in my life. A friend of mine who has had tons of them (from VS to VE, he has a VE maloo atm) has said that the gearboxs are noisy and rough but it shouldn't be making noise when releasing the clutch or something.
Other problems are obv the diff slap that happens (you can be starting to accelerate and it feels like the car isnt doing anything, then clunk from the rear and now it accels properly), i thought there was something wrong until my mate told me pretty much every commodore does it thats why he recommended getting the diff and gearbox changed to aftermarket set....tho that will probably void my warranty...
Sigh........
My 3000km inspection is up soon so hopefully I can somehow get them to give me a whole new box and clutch etc.