After help from Roger Koumans at Emprum LLC I got APGS upload working on my iPhone4 with iOS6.
Seems to be a problem with the daemon mentioned above, but a reboot of the iPhone solved it, for me I had to have UltimateGps opened before I connected the device to get it uploading AGPS data
After reboot and opening UltimateGps first I got it running smoothly
Thanks Roger K, hopefully iPhone will get an update to the IOS6 that handles the shutdown of the deamon that handles 30-pin connector..
/BoA