Originally Posted by jbtvt

In a vac system any pedal pressure releases vacuum on one side of a diaphram and makes the pedal easier to depress. In an electronic system they might use an on/off switch to mimic vacuum release, I don't know, but they could also use a resistance strip to gauge how much pressure the driver is trying to apply and ramp up pump pressure based on that. In that case, it seems possible that if you were getting too much (or too little depending on setup) voltage based on what the computer expects for that pedal position, that you could get a pump going wild and causing this. I'd also check the plugs for corrosion, esp given how corrosive brake fluid is.

My GS has the same type of system but a brief look in the FSM right now didn't turn up any pinout tests that could be done. I would absolutely let Lexus take a look at things. Those booster/cylinder units are very expensive, might as well get it taken care of under warranty, if that's the case. Trac/ABS as others suggested does make logical sense as well, I just find that harder to envision the mechanics of, personally. A competent tech with better info and wiring diagrams than we have available should be able to figure it out. Do post an update when you get it solved.