One problem related to noises during shifting has been reported for the 1999 Lexus RX300. The most recently reported issues are listed below.
Own a 1999 Lexus RX 300. Engine transmission has been sluggish since I purchased the car in 2001. Since we have owned the car we complained the dealer that when you start to run the car in the morning it will take a few minutes before the car will shift from 2nd to 3rd gear. The dealer kept telling us that was normal for the model car. The transmission got continually more sluggish over the years meaning that there was hesitation or jerky ness when you would pull your foot off of the gas. Last week I started to hear a grinding noise when the car was shifting from 2nd to 3rd gear. I just got back from the repair shop where I was told that the transmission which just turned 130,000 miles was shot and that the only fix was to purchase a rebuilt one from Lexus at a cost of $4,500 to $5,000. They told me they were aware that this was a common problem with 1999 - 2001 RX 300 transmissions but that there was never a recall or service bulletin issued. If this is a common problem then I think someone should do something about it.