I have a 1990 LS400 that developed the same problem - baffled me for months. It turned out to be a defective radiator.
These are aluminum radiators and have extremely small passages that are easily clogged if you inadvertently use or top off
with the wrong (i.e. non-Toyota) coolant. Some of these passages had become clogged in my radiator and it had to be replaced.
A new radiator solved the problem and is has never recurred.
I have exactly this same heater hot/cold issue with my '97 LS400. Thanks for the suggestions -- I'll check things out and let you know what I find.
Here is the answer, most likely for all Lexus owners. I have a 1994 SC400. No heat. I found a web posting at http://en.allexperts.com/q/Lexus-Repair-818/f_4590148.htm
Follow their directions. This fixed my heater. I think there is a fundamental flaw in the Lexus design. When the fluid level gets low you get a gas pocket that lives in the heater core. This keeps the fluid from flowing through the heater core. I loosened the 17 mm bolt at the top of the thermostat and ran the car at 2500 rpm. At the same time, have the coolant cap off and top off the coolant over and over until the coolant level is finally full. You will get heat after this. Retighten the 17 mm bolt, secure the coolant cap and be happy!
If this works, please pass it on. This will save a lot of Lexus owners a lot of grief and money. It took a total of five minutes to fix!! Yeah internet!!!!