I've had to have it jumped twice now and almost towed. Battery is fine, measures 12.5 volts. Had it tested at autozone too. But when I use Dr. Prius, it says the 12v is only 11.5, which is too low for it to go into ready mode. Where does this measurement occur at? I checked the positive and ground at the battery, it's fine. I get 12.2v at the jumper junction under the hood, all 3 were fine, no corrosion, not loose.
Pin sixteen of the OBD-II connector has 12 volts at all times. Many dongles provide a voltage reading by actually measuring that—not by asking any ECU in the car for a reading. It does seem as if there might be a substantial voltage drop between the battery and other stuff ... I'm not used to having much trouble going READY unless voltage drops below 8 or so.
The other odd thing I noticed is when it's acting up, the car beeps when you open the door until you close it.
I think I have it fixed. Pulled the connector out of the Transmission Control Unit and some of the metal was corroded, sprayed it with contact cleaner and brushed it. So far, so good. Oddly the pins on the control unit itself were still shiny.