Coding multiple effects controlled by rotary sw

Ok, see. I got it somehow working, but seems like this timer1 interruption interferes with the millis() function? As my timer gets corrupted once effect is used. Do you have any experience with that? Or maybe - is it possible to put the effect interrupt to timer0 or 2? If yes, how it can be done?

I tried to use the switch to control programs. This is the program i wrote but it doesn't work well: the switch donesn't change the effects. Is there something wrong?

//defining hardware resources.
#define LED 13
#define FOOTSWITCH 12
#define TOGGLE 2
#define PUSHBUTTON_1 A5
#define PUSHBUTTON_2 A4

//defining the output PWM parameters
#define PWM_FREQ 0x00FF // pwm frequency - 31.3KHz
#define PWM_MODE 0 // Fast (1) or Phase Correct (0)
#define PWM_QTY 2 // 2 PWMs in parallel

//other variables
int input, distortion_threshold=6000, vol_variable=512; //initial value adjusted by try and error.
int counter=0;
unsigned int ADC_low, ADC_high;

void setup() {
//setup IO
pinMode(FOOTSWITCH, INPUT_PULLUP);
pinMode(PUSHBUTTON_1, INPUT_PULLUP);
pinMode(PUSHBUTTON_2, INPUT_PULLUP);
pinMode(LED, OUTPUT);
pinMode(TOGGLE, INPUT);
// setup ADC
ADMUX = 0x60; // left adjust, adc0, internal vcc
ADCSRA = 0xe5; // turn on adc, ck/32, auto trigger
ADCSRB = 0x07; // t1 capture for trigger
DIDR0 = 0x01; // turn off digital inputs for adc0

// setup PWM
TCCR1A = (((PWM_QTY - 1) << 5) | 0x80 | (PWM_MODE << 1)); //
TCCR1B = ((PWM_MODE << 3) | 0x11); // ck/1
TIMSK1 = 0x20; // interrupt on capture interrupt
ICR1H = (PWM_FREQ >> ;
ICR1L = (PWM_FREQ & 0xff);
DDRB |= ((PWM_QTY << 1) | 0x02); // turn on outputs
sei(); // turn on interrupts - not really necessary with arduino
}

void loop() {
//Turn on the LED if the effect is ON.
if (digitalRead(FOOTSWITCH)==HIGH) digitalWrite(LED, HIGH);
else digitalWrite(LED, LOW);

//nothing else here, all happens in the Timer 1 interruption.
}

ISR(TIMER1_CAPT_vect)
{
// get ADC data
ADC_low = ADCL; // you need to fetch the low byte first
ADC_high = ADCH;
//construct the input sumple summing the ADC low and high byte.
input = ((ADC_high << | ADC_low) + 0x8000; // make a signed 16b value

if(digitalRead(TOGGLE)==HIGH)
{
counter++; //to save resources, the pushbuttons are checked every 1000 times.
if(counter==1000)
{
counter=0;
if (!digitalRead(PUSHBUTTON_2)) {
if (distortion_threshold<32768)distortion_threshold=distortion_threshold+25; //increase the vol
digitalWrite(LED, LOW); //blinks the led
}

if (!digitalRead(PUSHBUTTON_1)) {
if (distortion_threshold>0)distortion_threshold=distortion_threshold-25; //decrease vol
digitalWrite(LED, LOW); //blinks the led
}
}

//the input signal is 16bits (values from -32768 to +32768
//the value of input is clipped to the distortion_threshold value
if(input>distortion_threshold) input=distortion_threshold;

//write the PWM signal
OCR1AL = ((input + 0x8000) >> ; // convert to unsigned, send out high byte
OCR1BL = input; // send out low byte
}
else
{
//write the PWM signal
OCR1AL = ((input + 0x8000) >> ; // convert to unsigned, send out high byte
OCR1BL = input; // send out low byte
}
}