I have a 2013 ES 350 with 125K miles. Have had the transmission replaced twice now and it has failed again. The car has harsh upshift between 1st and 2nd gears and delayed engagement in 4th through 6th gears. Beyond a failure to properly reinstall the transmission, we have checked for electrical system problems and found none. There is something going on with the battery voltage (it keeps having a load drain) and I am wondering if anyone on this forum has experienced this combination of problems? At this point, I tend to believe it isn't simply improper installation but something deeper, like with the computer system, that is causing the problems. Hoping someone recognizes this pattern.

 

Some additional details would be helpful. Was the original transmission rebuilt and replaced, was a new/rebuilt transmission installed or was a used transmission installed? Was the torque converter replaced and cooling lines flushed? Were the transmissions reprogramed for your Lexus? Are there trouble codes being shown? Hopefully the replacement transmissions are covered by warranty.
The battery drain problem is likely unrelated but it can be diagnosed by a good mechanic checking each fused circuit to narrow down the cause. There are some good Youtube videos on this procedure if you are handy with tools.

 

A few q's? Were both Trans doing the same thing? Or better yet all 3? Who did the replacements and what fluid fill procedures did they use? Also when the FWD Trans have problems lots of times they damage the drive shaft Axles which are shafts into the trans lto the Trans differential which is built into the Trans on the ES350 FWD Trans.

You do Not have to have the Dealer reprogram the ECU or anything for the Trans. Might want to check the Trans ECU also. If were me I would take to a Toyota Dealer (less cost) to get checked out as they have all the Software and the Camry and Avalon use the same Engine/Trans as the ES350. What/where did you get the replacement Trans? Details about the 2 replacements?