Noises During Shifting problems of the 2003 Volkswagen New Beetle

I started experiencing transmission shift problems on my '03 vw beetle turbo, just around one year after purchase from a vw dealer. The vehicle was pre-certified at the time, since I couldn't afford the warranty, but the dealer had, I presume, declared it free of defects and problems. I took the vehicle back to the dealer to check the problem, upon which I was advised to replace the transmission at a cost of $4200. No further details were given as to the reason or possible cause for the problem, in spite of my requests for a description. The service advisor just stated "it needs to be replaced". I have since visited online automotive forums and found out this seems to be a problem with other owners as well. I am concerned now that even if I replace it, the replacement may have the same problem. In the mean time the transmission unpredictably starts slipping, or making a squeaking noise when slipping and at other times won't even shift for several seconds.