This happened to my Cic yesterday after I disconnected the battery. It was flaky for a while and I couldn't getthe top up. No alarm chirp, trunk wouldn't unlatch with the remote or the lever in the cab, but doors locked fine. My door windows wouldn't go up with the "all up" switch. I had to raise them individually.
After manually raising the top, everything returned to normal. With all that in mind, I agree that something came loose and your car had to "reset" itself.
2004 325CiC Convertible; Silver Gray Paint, Gray Leather, Black Top, Sport Package, Premium Package, Xenons, heated seats, but too cheap to buy the nav...
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