Ok, so this is my last resort, posting my story everywhere in the hope it doesn't happen to other people.
I own a '55 plate Seat Leon Cupra R, it has now covered 81,000 miles. When I purchased it there were ~78,000 miles on the clock and there was no noise to be concerned about. This was January 2013.
After a few weeks I noticed there was a rattle on the gearbox when the clutch was let out, down to the Clutch release bearing. I booked it into the garage and had a 3 week wait due to their being busy. By the time it went in there was a constant rattle whenever any throttle was applied and the gears weren't engaging as smoothly as before. Note: This car is not driven hard, just my plod to work where I manage 38-40mpg over 11 miles.
Ten minutes after I took it in there was a call to say that it was not just the CRB, he had spoken to his g/b specialist and it was a known fault in the top shaft. Agreeing to have it sent off for a intermediate rebuild at £400 I thought that was the end. This is a known fault and VAG made an adjustment to the box in '07.
Today I spoke to the gearbox specialists. He said "This is the worse condition VAG gearbox I have ever seen"(sic). I am now awaiting a £900 complete rebuild of the gearbox as "there is only one gear identified that could be re-used"(sic). The lateral play in the shaft has caused all the teeth to damage one another to the point they are pitted and it probably wasn't far off shattering a tooth. They are essentially getting a complete other gearbox and reconditioning that as mine is scrap!
I called SEAT head office customer services and they said as the car was not purchased from SEAT, it was out of warranty and they weren't repairing it, there was NOTHING they would be willing to do. If I took it in after for investigation it would be at my cost EVEN if they found it to be a manufacturing fault.
I have instructed the gearbox specialist to return the old g/b to me along with all the parts. I will be taking pictures and posting these, I then plan to take the g/b up to SEAT head office in Milton Keynes and tell them I am returning their seemingly sub-standard parts.
I love VAGs, I rate them VERY highly, however this experience and the fact a gearbox has literally eaten itself in no more than 4000 miles has changed my mind. I am digusted they wont even look into it! As some may notice, I also own an '89 mk2 Golf GTI and the gearbox in that has nothing more than a slight stick in second after 24 years and ~140,000 miles!
BEWARE ANYONE BUYING A VAG WITH A 6-SPEED BOX!