I would bet 95% that your I-Bus signal is not connected. Another guy just finished an E39 retrofit, and he had the exact same problem. In his case, it turned out to be a poor connection on the I-Bus pin to the nav computer. Here is his success post. If you search that forum, you will find his other posts describing the symptoms and what he did to debug it.
http://www.bimmerboard.com/forums/posts/251627/
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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
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