No output from pins

I am using a TivaC connected launchpad to program a breakout board with a TM4C1294NCDPT chip.  I am successfully able to flash it using LM Flash Programmer using *.bin files compiled from energia.  I have tried the first pin PD_0 and a few others like PN_0 and PF_4 but none of them would provide any output when set high.  I have tested the code on a connected launchpad and the code does work.

All the VDD, VDDC, GND, and pull up resistors are connected accordingly just like shown in the launchpad.  I have tried to add a 16Mhz crystal but it does not appear to make a difference.

Flashing always requires us to go through the Debug Port Unlock process.

After a few attempts, it wont go into the debug mode in Keil IDE anymore.

The chip and LP are isolated by removing the JTAG pins going to the launchpad so that the only thing connected to the chip is the 3.3v power and ground from the launchpad.  The pins that should go high only outputs 0.645V while on the launchpad it would have 3.3v.  We even used a hot air station to completely desolder a programmed TM4C1294 chip from the launchpad and resoldered it onto one of the breakout boards and only provide power but it still doesn't work.

When flashing the LM Flash programmer verified the memory and did a hardware reset and it still doesn't work.

Is the 25Mhz crystal required for the chip to be operational?  Also, is the 6mm distance max between the crystal and pin absolutely necessary?

Here is the sketch I used to test the pins using energia.

1. void setup() {
3. pinMode(PD_0, OUTPUT);
4. pinMode(PN_0, OUTPUT);
5. pinMode(PF_4, OUTPUT);
6. }
7. void loop() {
8. digitalWrite(PD_0, HIGH);
9. digitalWrite(PN_0, HIGH);
10. digitalWrite(PF_4, HIGH);
11. delay(1000);
12. digitalWrite(PD_0, LOW);
13. digitalWrite(PN_0, LOW);
14. digitalWrite(PF_4, LOW);
15. delay(1000);
16. }