It turns out that some of the wires in the top mechanism were rubbing and ended up shorting out one of the microswitches that's used to determine top position. The microswitch is only a $36 part. Yay!
The good news: my car has a CPO warranty and the warranty paperwork says that the top electronics are covered. I would only have to pay a $50 deductable on the $850 repair. Yay!
The bad news: BMW decided not to honor the warranty. I naturally pressed them for an explanation and they said that the repair would not be covered because the movement of the top caused the wiring to fail.
In summary: your BMW CPO warranty isn't worth the paper it's printed on because BMW can randomly decide what it covers and what it doesn't, regardless of what's printed in the warranty itself.
