Wow, these problems are still around.
I have a 2004 4Runner and I always plug in the OBD while the engine is running. I then turn the car off to read/erase codes, and only take the OBD off when the 4runner is back running. I just know it works and if I take the OBD off any other way, I am in some flat parking lot with the paper-clip...
The VSC 'turn-off' is from both a O2 'fail' and sometimes a fuel cap issue. I have seen both.
I have the wife not allowed to refuel it, that solves the gascap issue, and I have rigged the wiring on the O2 sensors to trick the ECU into seeing what it wants.
Basically, the two rear O2 sensors are just there post-catalytic converter to check that it is functioning. The scheme the vehicle uses is to run a bit rich after a number of highway miles (30 or so?), and it monitors the voltage on these cheap old school O2 sensors. If they indicate rich, then the ecu sends a code, disables the VSC etc. (they should be sued), and people run to the stealership.
I am an EE and it is very easy to just send a constant voltage signal that makes the ecu think it is seeing a good-cat condition.
This is a problem across many Toyotas and Lexus (I believe). The VSC is a critical safety system built into the vehicles. To disable it for a gascap or emissions issue is crazy. I once called up the Toyota engineers in the US, they said it is meant to save the engine! I told them fvck-the-engine, this is the 'baby-car' that my wife hauls my kid around in. It got pretty intense and I wish I taped that phone call!!!