... Using the pinguino toolchain, 2 LEDs now light up, and the debugger at least thinks that we're in the up_idle function, so that looks promising. After switching the serial console to UART2(for the explorer16), I do now get data out of the serial port! The last message that I see is "nx_start: CPU0: Beginning Idle Loop". Nothing else is happening though - I was expecting to get some kind of shell, as USER_ENTRYPOINT is set to "nsh_main".
That means that the OS bring-up completed without error but something failed while starting the application. Perhaps the memory is still configured wrong or perhaps the NSH stack size is too small. It is impossible to diagnose without debugging.
I would put a breakpoint on nsh_main and see if it gets there.