Temporarily reconnedt your MID to your car. Then the countdown will work. You need to get your car coded for nav so that the OBC coundown will work properly in the future. Here is someone who just had the identical problem in an E38.

http://www.bimmerboard.com/forums/posts/410650
http://www.bimmerboard.com/forums/posts/411022/

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2000 E38 750iL Highline Edition, Upgraded with the lastest 2006 X5 Electronics
MKIV Navigation, 16:9 Display, Bluetooth, TV/Video with Backup Camera, Sirius, and Aux Input