CCS/MSP430F5659: .map file shows flash section isn't populated with data set by SET_DATA_SECTION()

Part Number: MSP430F5659

Tool/software: Code Composer Studio

I'm using compiler TI v17.3.0 with CCS Version: 6.1.0.00104. Optimization Disabled

I'm using #pragma SET_DATA_SECTION to store arrays of data in sections I define in my cmd file. On inspection of the .map file, the sections exist, but no data is being stored in them. I am updating a project where this piece of code worked for a long time, below are the things that I have changed:

1. I just recently updated my compiler from TI v4.4.5 to gain additional support for time.h. 
2. I relocated the header file that sets the data sections

Here are snippets from my .cmd, .map, and .h file:

CMD 

SECTIONS
{
    .bss        : {} > RAM | RAM2           /* Global & static vars              */
    .data       : {} > RAM | RAM2           /* Global & static vars              */
    .TI.noinit  : {} > RAM | RAM2           /* For #pragma noinit                */
    .sysmem     : {} > RAM                  /* Dynamic memory allocation area    */
    .stack      : {} > RAM (HIGH)           /* Software system stack             */
    .fl_start	: {} > FL_JMP
    .fl_main	: {} > FL_MAIN
    .fl_version	: {} > FL_VER

....

MAP

******************************************************************************
                  MSP430 Linker PC v17.3.0                     
******************************************************************************
>> Linked Wed Jun 14 10:38:15 2017

OUTPUT FILE NAME:   <Evolution.out>
ENTRY POINT SYMBOL: "_c_int00_noargs_noexit"  address: 0000c8d4


MEMORY CONFIGURATION

         name            origin    length      used     unused   attr    fill
----------------------  --------  ---------  --------  --------  ----  --------
  SFR                   00000000   00000010  00000000  00000010  RWIX
  PERIPHERALS_8BIT      00000010   000000f0  00000000  000000f0  RWIX
  PERIPHERALS_16BIT     00000100   00000100  00000000  00000100  RWIX
  INFOD                 00001800   00000080  00000000  00000080  RWIX
  INFOC                 00001880   00000080  00000000  00000080  RWIX
  INFOB                 00001900   00000080  00000000  00000080  RWIX
  INFOA                 00001980   00000080  00000000  00000080  RWIX
  USBRAM                00001c00   00000800  00000000  00000800  RWIX
  RAM                   00002400   00004000  00000da0  00003260  RWIX
  FL_JMP                00008000   00000200  00000000  00000200  RWIX
  FL_VER                00008200   00000200  00000000  00000200  RWIX
  FL_MAIN               00008400   00004000  00000000  00004000  RWIX

......

Header File

#pragma SET_DATA_SECTION(".fl_start")
const char fl1[] = {0x32,0xC2, ...};
#pragma SET_DATA_SECTION()

#pragma SET_DATA_SECTION(".fl_version")
const char fl_ver[] = { 0x01,0x00,0x06,0x00};
#pragma SET_DATA_SECTION()

#pragma SET_DATA_SECTION(".fl_main")
const char fl2[] = {0xB1,0x00, ...}
#pragma SET_DATA_SECTION()

If you could point me in the right direction I would appreciate it.

Thanks,