AVR Freaks

Custom board with a ATSAMV71N19B. Calls to the HAL_Delay on one project are hanging because the SYSTICK count flag isn't getting set. SYSTICK is enabled and has a clock source in PMC. Created a small project with just some delay calls, and that's working fine. I've combed through and can't figure out what the difference is that's preventing SYSTICK from working in the one project. In both projects, I see the declaration of the handler but no definition. Clearly there is one, because it's working. What am I mising? 

Directly from START:

/**
 * \brief Delay loop to delay n number of cycles
 */
void _delay_cycles(void *const hw, uint32_t cycles)
{
	(void)hw;
	uint8_t  n   = cycles >> 24;
	uint32_t buf = cycles;

	while (n--) {
		SysTick->LOAD = 0xFFFFFF;
		SysTick->VAL  = 0xFFFFFF;
		while (!(SysTick->CTRL & SysTick_CTRL_COUNTFLAG_Msk)) //HANGS HERE
			;
		buf -= 0xFFFFFF;
	}

	SysTick->LOAD = buf;
	SysTick->VAL  = buf;
	while (!(SysTick->CTRL & SysTick_CTRL_COUNTFLAG_Msk))
		;
}