The issue with the stock alternator is the same as any other alternator: faulty voltage regulators. They're encased in an epoxy matrix and are internal on the type of alternators we have. If the epoxy isn't fully coating the circuit or there are voids/cracks then moisture will enter and cause failure. At the Ocala meet last year we were basically submerged in water and mud. Out of 11 VX's there were 3 that had alternator failure. Check out the photos: 2003 Ocala Meet.
This is the primary reason some are looking at a more robust and inexpensive replacement for the OEM unit. Not to mention MORE POWER!!! ;Dp;