Uninstalling NCSettings fixed my BT pairing w/Ford Sync
FWIW, I had the same problem in my 2010 Flex Sync w/Nav, would not pair with my JB'd iPhone 4 running 6.1.2, but it was pairing just fine with my JB'd iPad 2 running 6.1.2. I had NCSettings installed (on the iPhone only) but did not have Auxo, so I uninstalled NCSettings and now the iPhone 4 paired up just fine, plays audio makes/receives calls just fine.
Thx!