Great 
You will need this diagram:
On this digaram:
“3.3V LDO SRC” is S4.
“3.3V SRC” is S2.
You tried to power target CPU from LDO and LDO was set to EXT-DC, but without barrel jack.
If you power from the chipwisperer, use only “3.3V SRC” and turn off unnecessary LDOs, because all power comes from you USB port and you are powering a lot of different components and random problem can occur. From this reasons, I’m using barrel jack to do not worry about power issues anymore.
If you want to see better detailed diagram scroll down to the schematics on this site:
https://wiki.newae.com/CW308_UFO_Target