I had this happen 2 me about a year back. The car would shudder and not shift into the next gear or shift like it was being rammed from behind. I called Toyo and they said probably needs a new tranny (140000km on my car). I didnt even know about the ECU problem !! I ended up going to a tranny shop and it was a $5000 repair. Toyo woulda done it for $7000. Welcome to the RAV 4 world. This is pooor engineering in my opinion !!
Also, this year, my car has 183,000km, and there is major sludging in my engine. This caused an oil pump to my engine to fail, which lead to the cam gear on my VVTi enging not receiving lubrication. This ultimately led to the gear not functioning properly. Everytime the VVTi (variable valve timing) comes on, it causes the chain to stretch and knock against the valve cover. After opening up the engine and showing me what exactly is happening, I agreed and $2500 later, it's like a new car !! Im very disappointed in the amount of $ we all have to put into these vehicles post warranty (especially since it is not due to neglect of servicing).