The garage did fix the whine in 5th and 6th before I took delivery of the car, however, driving it home from the garage there was a speed related whine in all gears. Took it back to them and they initially replaced the diff but made no difference, then, and this was a time versus cost issue for them, simply swapped my gearbox for a reconditioned one and it's been right as rain ever since. The garage said they could have spent time replacing shims and bearings etc but as it's a trial and error game, the time it takes to strip the car and gearbox, refit and test until they find the problem, it was cheaper to simply swap boxes.
Looking at the bill the garage was sending to the warranty dept, I think £700 is a great deal for a recon and clutch, so I'd get it done before it lets you down or chews something. Good luck with it.