I feel your pain.... I've had some of the same problems with my mp3 player. Here is the best answer I can come up with.
First, when posting anything, it is important that you include your model, year, type of audio system, ( w/o Mark Levinson system), or navigation. It sounds like you might have one with navigation.
Lexus designed all of the sound systems, for all models, to inter face with "I-player" software. At first, I bought a Sansa mp3 player and had nothing but frustration trying to make the Lexus system do what I wanted to do. After calling several sources for answers, I bought a Ipad-Nano. Now everthing works perfertly. The Apple inter face software makes a big difference,
But....I found that all my mp3 files can not be transfered to the I pod Nano.
So my solution is I Pod.
Paul