PWM signal corrupted on pin 6 but not pin 5

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Ok, i've simplified my code and found that when it is running as i have posted then then led2 flickers like mad. however i can stop it from flickering by commenting out:

Serial.begin(9600);

or;

charge_state = digitalRead(charge_pin);

or;

strip.show();

or;

analogWrite(led1_pin,100);

so there seems to be some funny interaction between these processes. could anybody please help elucidate what might be happening now that i have posted my code? Cheers.

//neopixel library
#include <Adafruit_NeoPixel.h>
#ifdef __AVR__
#include <avr/power.h>
#endif


/////******PINS*****///////
//output pins
#define bc1_pin A1 //switch high to turn on the BC powering arduino, mp3 module, amp and neopixels
#define bc2_pin A0 //switch high to turn on servo BC
#define sink_pin A4 //switch low to sink current for voltage dividers and high to stop sinking(save current)
#define mos1_pin 10 // the audio Mosfet
#define mos2_pin 11 //servo mosfet 
#define neo_pin 12
#define mute_pin 13


#define led1_pin 5
#define led2_pin 6
#define ir_pin 9
#define ldr_pin A2
#define battery_pin A5
#define charge_pin A6
#define bagSwitch_pin A7


//////*******VAIABLES*******////////
bool handSwitch_state = false;
long ir_val = 0;
int ldr_val;
int battery_val;
bool charge_state;
int bagSwitch_val;

int battery_voltage;
int led2_val;

//PIN TOGGLES
bool bc1_tog = true;
bool bc2_tog = false;
bool mos1_tog = true;
bool mos2_tog = false;
bool led2_tog = false;
bool led1_tog = false;



///****OBJECT INSTANTATIONS****////
Adafruit_NeoPixel strip = Adafruit_NeoPixel(3, neo_pin, NEO_GRB + NEO_KHZ800);//create a neopixel object

void setup() {
//Serial.begin(9600);

  pinMode(bc1_pin, OUTPUT);  digitalWrite(bc1_pin, HIGH); //switch on the main boost converter
  pinMode(bc2_pin, OUTPUT);  digitalWrite(bc2_pin, LOW); //switch off the servo boost converter
  pinMode(sink_pin, OUTPUT); digitalWrite(sink_pin, LOW);
  pinMode(mos1_pin, OUTPUT); digitalWrite(mos1_pin, HIGH); //keep the mosfets off for the time being (rather than floating)
  pinMode(mos2_pin, OUTPUT); digitalWrite(mos2_pin, LOW);
  pinMode(mute_pin, OUTPUT); digitalWrite(mute_pin, HIGH); //set low to mute the amp
  pinMode(led1_pin, OUTPUT);
  pinMode(led2_pin, OUTPUT);


  pinMode(ldr_pin, INPUT);
  pinMode(battery_pin, INPUT);
  pinMode(charge_pin, INPUT);
  pinMode(bagSwitch_pin, INPUT);

  //neopixel begin
  strip.begin();
  strip.show(); // Initialize all pixels to 'off'


  strip.setPixelColor(0, 100, 50, 10);
  strip.setPixelColor(1, 20, 200, 30);
  strip.setPixelColor(2, 200, 20, 100);
  strip.show();
}



void loop() {



  analogWrite(led1_pin, 50);
  analogWrite(led2_pin, 100);



  strip.setPixelColor(0, 100, 50, 100);
  strip.setPixelColor(1, 0, 50, 20);
  strip.setPixelColor(2, 200, 100, 50);
  strip.show();




  ldr_val = analogRead(ldr_pin);
  //battery reading
  battery_val = analogRead(battery_pin);
  //charge status
  charge_state = digitalRead(charge_pin);
  //bagSwitch status
  bagSwitch_val = analogRead(bagSwitch_pin);

  battery_voltage = map(battery_val, 0, 1023, 0, 3284);
  battery_voltage = map(battery_voltage, 0, 3284, 0, 4200);


}