To make your USB design work at 3.3V, please select the power settings of the device as 3.3V/24MHz in the device editor. Also, please start the USB for USB_3V_OPERATION in main.c. If your design has the USB operating at 3.3V, please monitor the voltage at the VREG pin. If the voltage at the VREG pin is less that 3.3V, then remove the jumper at JP8 and adjust the potentiometer R22 till VREG gives 3.3V. Now you can give power to the device using power cord and place the jumper shorting VREG and VDD on P3.
Please go through the encoreIII board schematics to know the location of the jumpers.