AVR Freaks

Thanks for the response, I tried to change it but the problem remains. To be honest I'm not sure what the building process is I didn't change anything in atmel studio and I'm using atmel ice to upload the code, everything should be default, the only thing I changed was turning optimisations off because I thought it might optimize out some variable. Maybe I'm missing something in the PWM code, for the display to work PWM is needed and I made pin 16 the PWM pin, so maybe 

REG_PORT_DIR0 &= ~(PORT_PA05 | PORT_PA06 | PORT_PA07 | PORT_PA08 | PORT_PA09 | PORT_PA14 | PORT_PA15);

This line the right side of the expression is uint16_t and the rest of the bits get set to random values? However when Tried to save the the MSB half of the register

REG_PORT_DIR0 &= (~(PORT_PA05 | PORT_PA06 | PORT_PA07 | PORT_PA08 | PORT_PA09 | PORT_PA14 | PORT_PA15) | 0xffff0000);

The problem was the same, but when I saved PIN 15 aswell everything seems to work ok. I even tried to save ONLY the value of PIN 15 and everything is working as expected.
 

REG_PORT_DIR0 &= (~(PORT_PA05 | PORT_PA06 | PORT_PA07 | PORT_PA08 | PORT_PA09 | PORT_PA14 | PORT_PA15) | 0x00008000);

This is the complete code, I don't need to save the value when I make the pins inputs the second time, this is getting really confusing :D

bool toggleNumber(uint8_t numberToDisplay){
	// PWM is on PIN 16 and it's generated properly
	myPWM.begin();
	numberToDisplay = pinsettings.number[numberToDisplay];

	uint32_t pinDirections = 0, pinState = 0;

	for (uint8_t i = 0; i < 7; ++i) {
		// make all pins OUTPUTs and set them to LOW
		pinDirections |= (1 << pinsettings.segmentPinOrder[i]);
		pinState |= (1 << pinsettings.segmentPinOrder[i]);
	}
	// make the pins OUTPUTs and set them to LOW
	REG_PORT_DIR0 |= pinDirections;
	REG_PORT_OUT0 &= ~(pinState);

	myPWM.setOnPercent(45);

	DelayMs(10000);
	// make all pins INPUTs
	REG_PORT_DIR0 &= (~(PORT_PA05 | PORT_PA06 | PORT_PA07 | PORT_PA08 | PORT_PA09 | PORT_PA14 | PORT_PA15) | 0x00008000);
	pinDirections = 0x00;
	pinState = 0x00;

	for (uint8_t i = 0; i < 7; ++i) {
		if ((numberToDisplay >> i) & 1) {
			// set some pins to OUTPUT
			pinDirections |= (1 << pinsettings.segmentPinOrder[i]);
			pinState |= (1 << pinsettings.segmentPinOrder[i]);
		}
	}
	// set pins to HIGH
	REG_PORT_DIR0 |= pinDirections;
	REG_PORT_OUT0 |= pinState;
	// PWM = 55 to turn the display ON (45 OFF)
	myPWM.setOnPercent(55);
	DelayMs(10000);

	// set all pins to inputs
	REG_PORT_DIR0 &= ~(PORT_PA05 | PORT_PA06 | PORT_PA07 | PORT_PA08 | PORT_PA09 | PORT_PA14 | PORT_PA15);
	//REG_PORT_DIRCLR0 = (PORT_PA05 | PORT_PA06 | PORT_PA07 | PORT_PA08 | PORT_PA09 | PORT_PA14 | PORT_PA15);
	//DelayMs(60000 * 15);

	return true;
}

Just for clarity I'll post the PWM code aswell maybe I'm missing something 

Complete PWM code:
 

PWM::PWM(int freq) {

	_freq = freq;
	_period = 8000000/freq;
}

void PWM::begin(void) {

	PM->APBCMASK.reg |= PM_APBCMASK_TCC0; // Enables the APB clock inside Pwr Management for TCC0

	GCLK->GENCTRL.reg = GCLK_GENCTRL_IDC |			// Improve duty cycle
	GCLK_GENCTRL_GENEN |		// Enable gen clock
	GCLK_GENCTRL_SRC_OSC8M |	// Select prefered source (8 MHz oscilator in this case)
	GCLK_GENCTRL_ID(4);			// Select GCLK ID, in this case GCLK4

	while(GCLK->STATUS.bit.SYNCBUSY); // Wait until clock bus is synced

	GCLK->GENDIV.reg =	GCLK_GENDIV_DIV(1) |	// Divide clock by (in this case 1)
	GCLK_GENDIV_ID(4);		// Apply to selected clock

	while(GCLK->STATUS.bit.SYNCBUSY); // Wait until clock bus is synced

	GCLK->CLKCTRL.reg = GCLK_CLKCTRL_CLKEN |		// Enable gen clock
	GCLK_CLKCTRL_GEN_GCLK4 |	// Select clock
	GCLK_CLKCTRL_ID_TCC0;	// Feed the clock to wanted TCC

	while(GCLK->STATUS.bit.SYNCBUSY); // Wait until clock bus is synced

	TCC0->CTRLA.reg |= TCC_CTRLA_PRESCALER(TCC_CTRLA_PRESCALER_DIV1_Val); // Divide counter by 1 giving 8 MHz (125 ns) on each TCC0 tick
	TCC0->WAVE.reg = TCC_WAVE_WAVEGEN_NPWM; // Use "Normal PWM" (single-slope PWM): count up to PER, match on CC[n]

	while(TCC0->SYNCBUSY.bit.WAVE); // Wait for synchronization

	TCC0->PER.reg = _period; // Set the period (the number to count to (TOP) before resetting timer)

	while(TCC0->SYNCBUSY.bit.PER); // Wait for synchronization

	// Configure PA18 to be output
	PORT->Group[0].DIRSET.reg = PORT_PA16;
	PORT->Group[0].OUTCLR.reg = PORT_PA16;

	// Enable the port multiplexer
	PORT->Group[0].PINCFG[16].reg |= PORT_PINCFG_PMUXEN;

	// Connect TCC0 timer to PA18. Function F is TCC0/WO[2] for PA18.
	// Odd pin num (2*n + 1): use PMUXO
	// Even pin num (2*n): use PMUXE
	PORT->Group[0].PMUX[8].reg = PORT_PMUX_PMUXE_F;

	// Enable output (start PWM)
	TCC0->CTRLA.reg |= TCC_CTRLA_ENABLE;
	while(TCC0->SYNCBUSY.bit.ENABLE); // Wait for synchronization

}

void PWM::setOnPercent(float onPercent){
	if((onPercent >= 0) && (onPercent <= 100)) {

		TCC0->CC[2].reg = _period*onPercent/100; // Set starting PWM signal
		while(TCC0->SYNCBUSY.bit.CC2); // Wait for synchronization
	}
	else {

		TCC0->CC[2].reg = 0; // Set starting PWM signal to 0%
		while(TCC0->SYNCBUSY.bit.CC2); // Wait for synchronization
	}
}

Is pin 15 somehow connected to these PWM settings?