Hi Scott,
Can you confirm the following
1. In the function Proj_Peripheral_Config_ShutDown(); you are setting-clearint the Deep Sleep Clock Enable for the peripherals.
2. In the same function you are setting SysCtlPeripheralClockGating(true)
3. The Deep Sleep Clock Source is being set as MOSC
4. The debugger is disconnected (not just disconnect from the CCS window). The Debug Enable is a sticky bit in CM4. One sure shot way is to remove the power and then connect back the power
Regards
Amit