Just a quick update on my problems, which now seem to be solved.
I went back to the service department of my Lexus dealer and asked them for a road test with the foreman of the shop floor. When I arrived there and explained what I believe the problem was, the foreman said that he probably already knows what's wrong with the car and we even don't have to go for the road test. He asked if my battery was dead at some point in the past, and I confirmed it (I once left the interior light on over night, and the next day I couldn't start the car anymore and had to jumpstart it). So he said that the ECM was most likely the problem and he wanted to reset it so that it starts learning again. He also showed me a printout in which one item (I believe it was the ECM) was incomplete when I brought the car in, and complete after they fixed it. He also showed me a service document that listed some of the symptoms that I experienced, and the remedy for it (resetting of or relearning for the ECM). Since then my Lexus is performing well again, and the mileage is up to 28 to 29mpg from 21 to 22. I am very, very happy again with the car, and believe me, I was pretty upset before.
I was really happy with the service this time, but I am pretty disappointed with my last 20k service where I had already complained about the same problems, and they told me that they read back the diagnostics and couldn't find anything wrong with the car. I wonder what diagnostics they checked this time. Also last time when I picked up the car after the service and got into the car in the pickup garage, a service reminder popped up on the center display informing that a service (don't remember which one) is due. That also made me think how thorough the service was performed in the first place, and how serious they had taken my complaint that the hybrid doesn't work properly anymore.
Does any of you know if I always have to get the ECM reset if I drain my battery? If it has to be done, can it be done by the user or do I always have to take it to the Lexus service?
Here is a link I found to the TSIB on the ISC Learning procedure: http://autozone.kiev.ua/files/Lexus%20400H/Battery/data.pdf