External Power

J9 has to be in.

J9 is in, still no power

Did you connect the Gnd to the external power?

Check the voltage along the Blue lines shown below. The Black lines should not be connected.

I even measure 3.3v at J1 between ground and VCC

That means you succeeded in powering the target with external 3.3V.

What else did you do? What do you expect to happen?
Was the USB still connected to a PC? What about all the jumpers in J13?
Was there a Booster Pack or something plugged in?

I have downloaded a program with the USB and have verified the program runs.
I had expected the program that runs with the USB plugged in to run with the external 3.3 volt supply.
I have disconnected the USB from the computer.
I have not changed the configuration of the J13 jumpers.
I have a 3.3v voltage regulator circuit on a breadboard with sensor that I have paralleled the power to J12 ground and VCC.

Thanks for your thoughts

The "eZ-FET" section of the board gets power from the USB port of a PC. If it is not connected to a PC USB Port, it has no power.
The "target" section of the board gets power from your external 3.3V.
J13 is connecting the above two sections together. One has no power while the other has power. Neither section is going to work.