Do you have call waiting activated on your phone?
Do you have the nav or is it without?
Should only be to push the "answear"-button on the steeringwheel to take the new call.
See page 155 in the manual: http://drivers.lexus.com/t3Portal/document/omnav/OM76028U/pdf/u_05.pdf
They have some regulation about "If your cellular phone is not accepted for
HFP Ver. 1.5, this function can not be used." thou. Do you have a phone that have an older version of hands free profile perhaps?