Yes, you are not the only one experiencing this problem! See
https://discussions.apple.com/message/13298929#13298929 and i've seen more of these messages on the forums. But no exact cause or solution yet.
I'm having another but similar problem with my iPod Classic. I'm driving a F10 535d with 6FL option for connecting Apple iPhones/iPods. My iPod Classic 160GB plays slow after turning car off and on. It's about 7% slower than it ought to be. Also the playing time as displayed in the console is 'slower'. I bought a new iPod Classic 160GB. Same problem. Both the iPods work fine in a Audi Q5 with Apple Music Interface. And iPhones 3GS and 4 also work fine in the BMW. So my conclusion: the problem combination is the iPod Classic 160GB model in the BMW.
So, I think the problem is in the iPod indeed. Not in your copy though, but in the model. I expect a replacement with another copy of the same model will give the same problem.
So now, were are we to go with our problem? To BMW? But the BMW works fine with an iPhone. To Apple? But the iPod works fine in an Audi.
I've been resetting my iPod now about 50 or more times I think in the last 6 months.
Hope to hear from you if you find the exact cause or a solution