I had the same issue as described here. My old iPhone worked fine, then I bought 2 new iPhone 3Gs and upgraded the old iPhone to 2.0.
I re-paired everything and it seemed to work. As soon as I got back in the car, it could not find my iPhone. What was VERY interesting was that my wifes iPhone 3G and my sons old iPhone with 2.01 continued to work reliably.
No matter how many times I re-paired my iPhone, it would never reconnect automatically when I re-entered the car. After some research I came up with the following procedure that seems to fix the problem:
1 - Verify that your MYGIG radio has the latest firmware. If you are not sure or need to upgrade it go to this site for instructions:
http://mofv.com/MyGIG/
2 - Now press and hold both the up and down seek button and the Menu button at the same time to put the radio in engineering mode. This key combination is for the MYGIG RER. Different models may have different reset procedures so please check the afore-mentioned site if you have a different MYGIG radio.
BE VERY CAREFUL WHAT YOU DO FROM NOW ON.
3 - Look for and select the "Factory Defaults" option. In my RER radio it was on the second page.
The radio will erase all the user data meaning you will lose everything and need to re-enter your favorites and/or other settings. I do not know if you will lose any music you loaded on the internal hard drive as I do not use this feature.
4 - Shut down your iPhone completely by holding down the wake up button until you see the "Slide to power off" prompt. Turn off the phone by sliding the red arrow to the right.
5 - Now restart your iPhone and re-pair with the MYGIG.
So far it has worked the last 5 times I have used my car. I suspect that the profile was not properly erased or some such nonsense and subsequent re-pairings where half baked.
Let me know how it works for you guys!