There was one forum member that mentioned having the same issue with his iPod due to the heat from the tunnel area; he too stored his iPod in the center console and his iPod's internal HD crapped out
Not sure if it would help but possibly installing an aftermarket tunnel plate (something from Elite Engineering or LAPD) to cut down on console temps might be a solution. You would also get better chassis reinforcement to boot
I decided not to use the center console for storage of my iPod, I just throw it in the glove box. I have a docking station installed in the cupholder so when I'm using my iPod, it's physically connected in the cupholder dock. I need to keep the iPod within easy reach if I want to switch between songs since I'm still using the factory HU.
But since you have an Alpine HU, you don't need to have your iPod close by right (you control your iPod through your Alpine HU)? Maybe you should move it to the glove box...