TMS320F28027: Getting an accurate clock with a crystal

Hello forum,

I am trying to set up a TMS320F28027 C2000 microcontroller to act as an RTC for use in other functions on the chip. I have a crystal hooked up, and set up Timer2 to use the crystal. It seems to work, but I am not getting the accuracy that I am looking for.

It uses a 12 Mhz crystal that is supposed to be 15ppm, and I calculated the load capacitors to be 6pF using the formula C = 2(CL - Cstray), assuming 5pF Cstray, CL is 8pF.

The timer has a 11999 prescaler, which means the timer should count every 1ms * period, which means it should trigger every second, which just adds 1 to a 32 bit number. It seems that after 20 hours, it is 20 seconds out, which is 0.0556% or 556ppm, not even close to the expected 15ppm!

This is the first time I have implemented a crystal in my design, so I'm not 100% sure I am doing it right, or really what accuracy I should be able to expect. I should also mention that it is powered off of a 3.3V  buck regulator, and the jtag debugger is attached and connected. I'm not sure if this changes anything, like does the debugger supply a clock that overrides any crystal?

Anyways, does anyone have any ideas or advice as to why I'm not getting the accuracy I need, or is my expectation unreal, and I should just get a dedicated clock chip? I would prefer to not have a separate chip if at all possible.

The crystal: https://www.digikey.ca/product-detail/en/avx-corp-kyocera-corp/CX3225SB12000D0GZJC1/1253-1696-1-ND/5995243

The Capacitors: https://www.digikey.ca/product-detail/en/tdk-corporation/C1608C0G1H060D080AA/445-5037-1-ND/2093652

The (relevant) board layout:

The Code:

uint32_t clock_period = 1000; //in ms
uint32_t clock_time_s = 0; //in s
uint32_t clock_time_s_offset = 0;

void initClockTimer()
{
	myTimer2 = TIMER_init((void *)TIMER2_BASE_ADDR, (size_t)sizeof(TIMER_Obj));

	EALLOW;
	PIE_registerSystemIntHandler(myPie, PIE_SystemInterrupts_TINT2, (intVec_t) &clockInterrupt);
	EDIS;

	TIMER_stop(myTimer2);

	CLK_setTimer2Src(myClk, CLK_Timer2Src_ExtOsc);
	TIMER_setPeriod(myTimer2, clock_period);
	TIMER_setPreScaler(myTimer2, 11999);
	TIMER_reload(myTimer2);
	TIMER_setEmulationMode(myTimer2, TIMER_EmulationMode_RunFree);

	TIMER_enableInt(myTimer2);

	TIMER_start(myTimer2);

	CPU_enableInt(myCpu, CPU_IntNumber_14);

	Clock_setPosixTime(1447459200);
}

void Clock_setPosixTime(uint32_t t)
{
	clock_time_s_offset = t - clock_time_s;
}

#pragma CODE_SECTION(clockInterrupt, "ramfuncs");
__interrupt void clockInterrupt(void)
{
	GPIO_toggle(myGpio, GPIO_Number_0);

	clock_time_s++;
}