Flash File system

I am using a RCM2100 with 512MB ram and 512 MB flash
I have a program which uses the flash file system. When I run code compiled from the IDE, fs_get_flash_lx() returns 1. When I compile using the command line compiler using the following command:
dccl_cmp.exe" “%src%\Timekeeper3.c” -pf “%rtifile%\F6050.dcp” -rf “%rtifile%\F6050.rti” -lf “%RabRel%lib.dir” -rti 0x0700:2000r3:11.0592:512:512 -d “NODEBUG” >> compile.log

fs_get_flash_lx() returns 0 when trying to initialize the flash system. The rti and dcp files are the same in both cases.

Where does one start in order to find the reason for this?