The hand held scanner will probably not turn up any codes. You will have to have a more in depth scanner/data logger to actually see what is going on. With the O/D flashing, there is something wrong, but it will be hard to put your hand on it.
To keep from throwing parts at this thing, I would take it to a shop and have them test drive the car with a data logging style scanner. That way, they can watch each of the sensors when the problem occurs and see any fault codes that might arise at the same time, but not stored into memory.
Then again, if you have access to a pressure tester and maybe someone with Alex Peppers OBD-II software and a laptop, then you might be able to pinpoint the problem.
If I had to guess at your problem though, I would first suspect maybe either a sticking #2 shift solenoid on the solenoid block or a sticking piston in the valve body. I would first try changing the fluid, just to see it helps for now though.
