Sorry, I forgot to mention I am using the JN-AN-1229.
My problem is the lack of mention of interrupt handling in the stack user guide. Whereas when using JN-AN-1184, the documentation specifically mentions the application of u32AHI_Init when using JenOS. As you can see, u32AHI_Init is not called for the JN516x when using ZigBee 3.0. The TARGET_INITIALISE() function is, to my untrained eyes, what appears to be a lot of vector macros which I do not understand. Hence the request for documentation on irq_JN516x.S.
Are you using the irq_JN516x.S file?
If not, what does the code below look like for you?
PUBLIC void APP_vSetUpHardware(void)
{
#if (JENNIC_CHIP_FAMILY == JN517x)
u32AHI_Init();
vAHI_InterruptSetPriority(MICRO_ISR_MASK_BBC, NVIC_INT_PRIO_LEVEL_BBC );
#else
TARGET_INITIALISE();
/* clear interrupt priority level */
SET_IPL(0);
portENABLE_INTERRUPTS();
// vAHI_BrownOutConfigure(E_AHI_VBOREF_3V0, FALSE, TRUE, FALSE, TRUE);
// vAHI_SysCtrlRegisterCallback( APP_isrSysCon );
// vAHI_InterruptSetPriority( MICRO_ISR_MASK_SYSCTRL, 4);
// u32AHI_Init();
#endif