Hi Martin,
I ran into the same problem as Tanmayee, but I found a solution.
When running a debug from RAM, the project would work correctly, but if the target was FLASH, the TRK would get stuck in an infinite loop, specifically the init_12sram_loop in MPC5643L_HWInit.c. It was because LOCKSTEP_MODE (which is what we're running) isn't defined anywhere, so HWInit.c was defaulting to DPM.
Adding the line #define LOCKSTEP_MODE in MPC5643L_HWInit.h fixed it for me, and the TRK runs the project from FLASH properly.
If you know of a better (or proper place) to put the LOCKSTEP_MODE flag besides the header file, please let me know.
Hope this helps someone out there.
Thanks