Just bought an 06 IS 250 and have noticed the same thing. AM stations are considerably lower volume than FM, a CD, or my Aux connection. My guess is that's just the lower power AM signal not getting a boost from the Lexus stereo.
I thought only people who drove Buicks and Lincolns listened to AM radio!?
2011 IS350 Matador Red Mica with spoiler, Nav, F sport exhaust, tint, Joe Z Intake in Blue, 8500 x50 radar detector, blend mount, smart card key, rear F sport sway bar, and steering damper.