Haven't had a similar problem, although there is anothe thread running currently about early clutch failures.
Has the dealer explained what the "gearbox problem" is? They sound a bit vague to me. 10,000 miles on a clutch is NOT acceptable though .... if I was a cynic I might think the dealer was trying to book your sons car in for some spurious gearbox work to recoup some costs that ARUK told them they would have to pay for bad workmanship when they changed the clutch the first time. Luckily I don't have a suspicious mind lol
You need more detail on this "gearbox problem" and if you can't detect anything, go to another dealer for a 2nd opinion