Okay, I'm going to be as specific as possible by setting up the situation where I have this problem. So let's say I'm talking to my girlfriend through the car and my roommate calls and I can either ignore him or accept the call.
1st situation: Accept the call. When I do this, and my girlfriend hangs up on the other line, the call with my roommate will end.
2nd situation: Ignore the call. Once my roommate's call is no longer "beeping in" the call with my girlfriend will end.
So basically when either of the partys on the line hang up, the call ends.
I have the Motorola RAZR, and this does not happen except when I am using the Bluetooth function on the car. I have a bluetooth headseat as well and this situation does not occur while using it. I took the car to the dealership and they had no idea what to do. I hope this isn't one of those situations where neither Motorola nor Lexus will accept responsibility and just point the finger at eachother. Any input is appreciated.

 

Go to lexus.com, phone stuff, find your specific phone and the pdf for BT connection instructions. It (for the Razr V3) says for problems with call-waiting, you might need a new software version from Cingular (if you have a V3 and Cingular).