Error on PWM output while using ATMega328p-au and Atmel Studio

Question

Hallo everyone, 

I am new into AVR programming and I was asked to develop a board which could read out the values of an analog sensor and set a PWM output. The design included a potentiometer, to act as a percentage dimmer between two PWM signals. 

As my programming experience is only in the Arduino IDE, when migrating to Atmel Studio 7 I used the import Arduino Code option and proceed with ISP programming using Atmel ICE. 

The model itself is composed of two analog signals (sensor and potentiometer) and 4 pwm outputs (two pairs of signals). Moreover, the code is based on a basic State Machine:
1) Read Sensor and Potentiometer, which determines the PWM output value. 
2) Case 1: increase the PWM output value
3) Case 2: decrese the PWM output value
4) Case 3: mantain the PWM output value

However, whenever I put the sensor under my Lamp (controlled by the PWM) it starts to flicker and I can not reach a "stable state". My posible solution would be read out the sensor's value and have an average between the highest and lower value, which will be later used to set the PWM output level and a second one would be using interrumptions but I do not know how to implement them. 

Note: the frequency is set to 10 MHz because I am using 3,3 V, so the cristal was selected according to the input value

/*Begining of Auto generated code by Atmel studio */
#define F_CPU 10000000UL
#include <avr/io.h>
#include <util/delay.h>
#include <Arduino.h>

/*End of auto generated code by Atmel studio */

//Pinout
const int C1 = 9;                     // Select the pin for Channel 1 PWM Dimming (Sunrise)
const int C2 = 6;                      // Select the pin for Channel 2 PWM Dimming (Daylight)
const int C3 = 5;                      // Select the pin for Channel 3 PWM Dimming (Sunrise 2)
const int C4 = 3;                      // Select the pin for Channel 4 PWM Dimming (Daylight 2)
const int CM = A1;                     // Select the pin for the color mixer (Potentiometer)
const int ALS = A0;                    // Select the pin for the ALS signal

//Variables
int ch = 0; // Current PWM level
int count = 0;
float ch1 = 0; // Color mixer factor of the Channel 1 and 3 PWM (0% - 100%)
float ch2 = 0; // Color mixer factor of the Channel 2 and 4 PWM (0% - 100%)
int mixer = 0; // Potentiometer value
int pwm = 0;   // PWM counter 
int th = 200;  // Threshold value (light sensitivity)
int als = 0;   // Stores the value of the ALS
int mst = 0;   // Maschine state
int sum = 0;   // Average ALS value
int sum2 = 0;  // Average trimmer value
int wait = 100; // Delay value
int f = 0; //1 Machine State counter
int i = 0; //2 Machine State counter

//Setup
void setup() {
//  I/O Pins
pinMode(C1, OUTPUT);
pinMode(C2, OUTPUT);
pinMode(C3, OUTPUT);
pinMode(C4, OUTPUT);
pinMode(ALS, INPUT);
pinMode(CM, INPUT);

//  Set PWM outputs to LOW
analogWrite(C1, ch1);
analogWrite(C2, ch2);
analogWrite(C3, ch1);
analogWrite(C4, ch2);
//Serial.begin(9600);
}

void loop() {

//State machine init
switch(mst){
    case 0:
    // Read the value from the Ambient Light Sensor and the Mixer Pin
    for(int i =0; i<wait; i++){
        delay(0.00001);
        als = analogRead(ALS);
        sum = als + sum;
    }
    
    // Obtain an average ALS value
    sum = sum/wait;
    mixer = analogRead(CM);
    
    //Serial.println(sum2);
    if(sum > th) {
        sum = th;
    }
    if(mixer >= 1000) {
        mixer = 1000;
    } else {

    }
    // Re-map average value to PWM level (0-255 == 0-100%)
    pwm = map(sum, 0, th, 255, 0);
    
    
    //Declare the color mixer percentage 
    if((mixer>=0)&&(mixer<512)){
        ch1 = 100;
        ch2 = (100*mixer)/512;
        } else if(mixer<1022) {
        ch1 = map(mixer, 512, 1000, 100, 0);
        ch2 = 100;
        } else {
        ch1 = 0;
        ch2 = 100;
        }
        
    //Serial.print(mixer);
    ch1 = ch1/100;
    ch2 = ch2/100;
    
    //Increase PWM
    if(ch<pwm-5){
    mst = 1;
    }
    
    //Change to the second stage
    if(ch>pwm+5){
        mst = 2;
    }
    
    //Change to third stage
    if((ch > pwm-5) && (ch < pwm+5)){
        mst = 3;
    }
    delay(0.000001);
    break;

    case 1: //Current PWM level less than the actual ALS value
        //Compare PWM and ch1 to make a gradual change
        count = ch+3;
        if (count > 255)
        {
            count = 255;
        }
        ch = count;
        analogWrite(C1, (ch*ch1));
        analogWrite(C2, (ch*ch2));
        analogWrite(C3, (ch*ch1));
        analogWrite(C4, (ch*ch2));
        delay(0.0000001);
        //Return to initial state
        mst = 0;
    break;

    case 2: //Current PWM level greater than the actual ALS value
        //Compare PWM and ch1 to make a gradual change
        count = ch-3;
        if (count < 0)
        {
            count = 0;
        }
        ch = count;
        analogWrite(C1, (ch*ch1));
        analogWrite(C2, (ch*ch2));
        analogWrite(C3, (ch*ch1));
        analogWrite(C4, (ch*ch2));
        delay(0.0000001);
        //Return to initial state
        mst = 0;
    break;

    case 3: //Current PWM level equal than the actual ALS value
        //Keep tha output value
        analogWrite(C1, (ch*ch1));
        analogWrite(C2, (ch*ch2));
        analogWrite(C3, (ch*ch1));
        analogWrite(C4, (ch*ch2));
        //Return to initial state (Read ALS & Trimmer)
        mst = 0;
        delay(0.0000001);
    break;

    default:
    //Empty
    break;
}
}