F28M36H33B2: Blinky example Flash-Standalone works on ControlCard but not on my target device

I have been developing my code using only RAM build. Now that I want to put it on the flash for standalone operation, it does not work.

I reverted back to the blinky example code, it works perfectly on the controlCard with concerto F28M36P63C2. I build flash-standalone, load it, remove the emulator, reset and both led's start flashing. When I load the exact same flash-standalone build blinky example code on my target device, which is a concerto F28M36H33B2, and only change the pin definitions since my led's are on different pins, it does not work. I know the code works fine because when I do a RAM build it works on my target device, both the blinky example and my own code. Also when I do a flash build (not standalone) on both M3 and C28, it also works when I start it with the debugger, but obviously if I remove the debugger and reset only the M3 starts because it does's send the boot command to the C28.

So in summary, when I load the flash-sandalone blinky example code on the controlCard it works, but on my own device it doesn't work, none of the led's start blinking when I reset it. Why would that be, the only difference is the concerto devices? Do I have to change something in the command linker file when I move from the controlCard to my target device? I use the blinky example v206 in controlSuite.  

Thanks

Albert