I also have a Ford Focus equipped with Microsoft Sync and I too have auto connect problem after Andriod 4.3 update. I have re-paired the SYNC from scratch but unfortunately, my S3 still will not auto connect to Microsoft Sync in my Ford Focus. I've since done a little bit of poking around. As far as I can tell, there are properties/settings for each paired bluetooth device on the S3. I don't think they were there pre 4.3 update but I could just not have noticed. For example, the paired device, SYNC, has "profiles" (that's what these two settings are under on the S3) "Call audio" and "Media audio". The description on "Call audio" and "Media audio" are "Use for phone audio" and "Use for media audio" respectively. Both are turned off by default. I've experimented and have found that with these profiles enabled, the bluetooth will connect automatically. Logically, for what I was trying to do, I believe I only need "Call audio" but at this point I don't really care. Here's what my challenge is, these "profiles" don't stay enabled. The bluetooth was working normally one day. The next day when I used the car again, bluetooth wouldn't work. Saw that both "Call audio" and "Media audio" were not enabled. Enabled them and the bluetooth was able to connect successfully.
I don't know how to make these setting sticks. Does anyone know how?