Multiple LED At Once

We already have a working product

We have started a new project, and are admittedly quite stuck.

Not to be nit picky , but when you read the above statements , don't they seem to contradict each other ?
Either the product is working or it is not . (admittedly the issues you are have sound trivial but nevertheless they are issues)
How can you in the same sentence say the product is working and that your are stuck ?
Which is it ?

I added some extra leds and made some changes:

int startup_led1 = 2;
int startup_led2 = 3;
int startup_led3 = 4;
int startup_led4 = 5;
int startup_led5 = 6;
int startup_led6 = 7;
int special_led7 = 8;
int special_led8 = 9;
int special_led1 = 10;


int brightness   = 5;

int fade         = 5;

unsigned long starttime;
unsigned long endtime;

long randON = 0;
long randOFF = 0;
int  randLED = 0;

void setup()
{
  pinMode(startup_led1, OUTPUT);
  pinMode(startup_led2, OUTPUT);
  pinMode(startup_led3, OUTPUT);
  pinMode(startup_led4, OUTPUT);
  pinMode(startup_led5, OUTPUT);
  pinMode(startup_led6, OUTPUT);
  pinMode(special_led7, OUTPUT); 
  pinMode(special_led8, OUTPUT); 
   pinMode(special_led1, OUTPUT); 
  
  randomSeed (analogRead (0)); 
  
 
}

void loop()
{
   digitalWrite(startup_led1, HIGH);   // turns the LED on
   digitalWrite(startup_led1, LOW);    // turns the LED off
   digitalWrite(startup_led2, HIGH);   // turns the LED on
   delay(30);                // waits for a second
   digitalWrite(startup_led2, LOW);    // turns the LED off
   delay(30);    
   digitalWrite(startup_led3, HIGH);   // turns the LED on
   delay(30);               // waits for a second
   digitalWrite(startup_led3, LOW);    // turns the LED off
   delay(30);    
   digitalWrite(startup_led4, HIGH);   // turns the LED on
   delay(30);               // waits for a second
   digitalWrite(startup_led4, LOW);    // turns the LED off
   delay(30);    
   digitalWrite(startup_led5, HIGH);   // turns the LED on
   delay(30);               // waits for a second
   digitalWrite(startup_led5, LOW);    // turns the LED off
   delay(30);    
   digitalWrite(startup_led6, HIGH);   // turns the LED on
   delay(30);               // waits for a second
   digitalWrite(startup_led6, LOW);    // turns the LED off
   delay(30);    
   digitalWrite(special_led7, HIGH);   // turns the LED on
   delay(30);               // waits for a second
   digitalWrite(special_led7, LOW);    // turns the LED off
   delay(30);    
   digitalWrite(special_led8, HIGH);   // turns the LED on
   delay(30);               // waits for a second
   digitalWrite(special_led8, LOW);    // turns the LED off
   delay(30);    
   digitalWrite(special_led1, HIGH);   // turns the LED on
   delay(30);               // waits for a second
   digitalWrite(special_led1, LOW);    // turns the LED off
   delay(30);    
  
 /////////////////////////////////////////////////////////////////
 
  
  for (int i=0;i<4;i++)
  {
   digitalWrite(startup_led1, HIGH);   // turns the LED on
   digitalWrite(startup_led2, HIGH);   // turns the LED on
   digitalWrite(startup_led3, HIGH);   // turns the LED on
   digitalWrite(startup_led4, HIGH);   // turns the LED on
   digitalWrite(startup_led5, HIGH);   // turns the LED on
   digitalWrite(startup_led6, HIGH);   // turns the LED on
   digitalWrite(special_led7, HIGH);   // turns the LED on
   digitalWrite(special_led8, HIGH);   // turns the LED on
   digitalWrite(special_led1, HIGH);   // turns the LED on

  ////////////////////////////////////////////////////////////////
  delay(80);    
  ////////////////////////////////////////////////////////////////
  digitalWrite(startup_led1, LOW);    // turns the LED off
  digitalWrite(startup_led2, LOW);    // turns the LED off
  digitalWrite(startup_led3, LOW);    // turns the LED off
  digitalWrite(startup_led4, LOW);    // turns the LED off
  digitalWrite(startup_led5, LOW);    // turns the LED off
  digitalWrite(startup_led6, LOW);    // turns the LED off
  digitalWrite(special_led7, LOW);    // turns the LED off
  digitalWrite(special_led8, LOW);    // turns the LED off
  digitalWrite(special_led1, LOW);    // turns the LED off
  delay(80);
  }
 
  //////////////////////////////////////////////////////////////// 
 for (int i=0;i<255;i++)
 {
  brightness = brightness ++;
  analogWrite(special_led1, brightness);
  delay(10);
  }
 analogWrite(special_led1, 255);
  for (int i=255;i>0;i--)
 {
  brightness --;
  analogWrite(special_led1, brightness);
  delay(10);
  }
 
  for (int i=0;i<255;i++)
 {
  brightness = brightness ++;
  analogWrite(special_led7, brightness);
  analogWrite(special_led8, brightness);
  delay(10);
  }
  
  analogWrite(special_led7, 255);
  analogWrite(special_led8, 255);
 
  for (int i=255;i>0;i--)
 {
  brightness --;
  analogWrite(special_led7, brightness);
  analogWrite(special_led8, brightness);
  delay(10);
  }
  
  starttime = millis();
  endtime   = starttime;
 
 while(brightness <= 1000)
 {
     while((endtime - starttime) <= 10000)
         {
           randON = random(90,90); //tweak these for faster blink
           randOFF = random(150,350); //tweak these for faster blink
           randLED = random(1,6);
 
               if(randLED == 1)
                  {
                     digitalWrite(startup_led1, HIGH);
                     delay(randON);
                     digitalWrite(startup_led1, LOW);
                     delay(randOFF);
                   }
 
               if(randLED == 2)
                 {
                   digitalWrite(startup_led2, HIGH);
                   delay(randON);
                   digitalWrite(startup_led2, LOW);
                   delay(randOFF);
                   }
 
                   if(randLED == 3)
                      {
                       digitalWrite(startup_led3, HIGH);
                       delay(randON);
                       digitalWrite(startup_led3, LOW);
                       delay(randOFF);
                       }
 
                   if(randLED == 4)
                     {
                     digitalWrite(startup_led4, HIGH);
                     delay(randON);
                     digitalWrite(startup_led4, LOW);
                     delay(randOFF);
                     }
 
                   if(randLED == 5)
                     {
                     digitalWrite(startup_led5, HIGH);
                     delay(randON);
                     digitalWrite(startup_led5, LOW);
                     delay(randOFF);
                     }
 
                    if(randLED == 6)
                       {
                       digitalWrite(startup_led6, HIGH);
                       delay(randON);
                       digitalWrite(startup_led6, LOW);
                       delay(randOFF);
                       endtime = millis();
                       }
 
 
          }
    }
}

Here's a link to a true random number generator library
https://code.google.com/p/avr-hardware-random-number-generation/