Working on making things stable

My current task is getting the darn thing stable, in some enviroments it works perfectly; in others, not so much.

Environment 1:
OS CentOS 6.6 (running as a VirtualBox guest)
Apache version: 2.2.15
PHP version: 5.3.3
Result: fairly stable, very rarely do I not get a sensor reading

Environment 2:

OS: CentOS7.1 (tried both a dedicated physical machine and a VirtualBox guest)
Apache version: 2.4.6
PHP version: 5.4.16
Result: When I take a reading of my photoresistor, one or both of my two LED's turns off/on. Sometimes I do not get a sensor reading.

Environment 3:

OS:Raspbian
Apache version:2.2.22
PHP version:5.4.39
Result: When I take a reading of my photoresistor, one or both of my two LED's turns off/on. Sometimes I do not get a sensor reading.

I've tested things under Minicom and all works well, which tells me the issue is on the PHP side of things.

Arduino code:

//temp sensor vars
boolean neg=0;
byte temp=0;
float tempb=0;
// end

byte hybyte=0;
int result=0;
void setup() {
  // put your setup code here, to run once:
DDRD|=B11000000; //setting pins 20 and 21 as outputs
ADMUX=B01000111;//set adc reference and select channel
ADCSRA=B10000110;//enable adc and set prescaler to divide by 64
//temp sensor pins
PORTC |=B11000000;
DDRC |=B11000000;// pc7 as ada and pc6 as sck
//end
Serial.begin(9600);
DS1631startconvert();
}

void loop() {
  // put your main code here, to run repeatedly:
//cal = OSCCAL;
if (Serial.available()){
     int ser = Serial.read();
    
     if (ser == 52){//keyboard key 4 to read the temp sensor
      DS1631readtemp();
      delay(50);
      tempb=(tempb*(9.0/5.0))+32;
      Serial.println(tempb,4);//4 decimal places 
      neg=0;
      temp=0;
     tempb=0;
       }
     else if (ser == 53){//keyboard key 5 to turn on led1
      PORTD |=B01000000;
      delay(50);
    Serial.println("Object1 enabled"); 
       }
     else if(ser == 54){//keyboard key 6 to turn off led1
      PORTD &=~B01000000;
            delay(50);
      Serial.println("Object1 disabled"); 
       }
     else if(ser == 55){//keyboard key 7 to turn led2 on
      PORTD |=B10000000;
            delay(50);
       Serial.println("Object2 enabled"); 
       }
      else if(ser == 56){//keyboard key 8 to tourn led2 off
      PORTD &=~B10000000;
            delay(50);
     Serial.println("Object2 disabled"); 
       }
       else if(ser == 57){//keyboard key 9 to read the photoresistor
            delay(50);
            adcread();
     Serial.println(result); 
       }
}

}

void adcread(){
ADCSRA |= (1 << ADSC);         // start ADC measurement
    while (ADCSRA & (1<<ADSC)); // wait till conversion complete 
result=ADCW;

}
//temp sensor reading
void start(){
DDRC|=_BV(DDC7);
PORTC|=_BV(DDC7);
PORTC|=_BV(DDC6);
PORTC&=~_BV(DDC7);
PORTC&=~_BV(DDC6);
}

void stop1(){
DDRC|=_BV(DDC7);
PORTC&=~_BV(DDC6);
PORTC&=~_BV(DDC7);
PORTC|=_BV(DDC6);
PORTC|=_BV(DDC7);
  }
void clk(){
PORTC|=_BV(DDC6);
PORTC&=~_BV(DDC6);
//delay(1);
  }
void DS1631startconvert(){
start();
//send address
//digitalWrite(sda,HIGH);
PORTC|=_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,HIGH);
PORTC|=_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,HIGH);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,LOW);//write
PORTC&=~_BV(DDC7);
clk();
//ignore ack
clk();
//start t convert command
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,HIGH);
PORTC|=_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,HIGH);
PORTC|=_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,HIGH);
PORTC|=_BV(DDC7);
clk();
clk();//ignoring ack
stop1();
}
void DS1631readtemp(){
start();
//send device address
//send address
//digitalWrite(sda,HIGH);
PORTC|=_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,HIGH);
PORTC|=_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,HIGH);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,LOW);//write
PORTC&=~_BV(DDC7);
clk();
//ignore ack
clk();
//send read temp command AAh
//digitalWrite(sda,HIGH);
PORTC|=_BV(DDC7);
 clk();
 //digitalWrite(sda,LOW);
 PORTC&=~_BV(DDC7);
 clk();
 //digitalWrite(sda,HIGH);
 PORTC|=_BV(DDC7);
 clk();
 //digitalWrite(sda,LOW);
 PORTC&=~_BV(DDC7);
 clk();
 //digitalWrite(sda,HIGH);
 PORTC|=_BV(DDC7);
 clk();
 //digitalWrite(sda,LOW);
 PORTC&=~_BV(DDC7);
 clk();
 //digitalWrite(sda,HIGH);
 PORTC|=_BV(DDC7);
 clk();
 //digitalWrite(sda,LOW);
 PORTC&=~_BV(DDC7);
 clk();
 clk(); //ignoring ack again
 stop1();
 start();
 //send device address
//digitalWrite(sda,HIGH);
PORTC|=_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,HIGH);
PORTC|=_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,HIGH);
PORTC&=~_BV(DDC7);
clk();
//digitalWrite(sda,HIGH);//read
PORTC|=_BV(DDC7);
clk(); 
//pinMode(sda,INPUT);//change pin from output to input for readin
DDRC&=~_BV(DDC7);
byte raw=0;
clk();
//read the temp
 //raw=digitalRead(sda);
 raw=PINC & _BV(PC7);
 if(raw==128){
  temp=temp+128;
 neg=1; 
 }
 clk();
 //raw=digitalRead(sda);
 raw=PINC & _BV(PC7);
 if(raw==128){
   temp=temp+64;
 }
 clk();
 //raw=digitalRead(sda);
 raw=PINC & _BV(PC7);
 if(raw==128){
  temp=temp+32; 
 }
 clk();
 //raw=digitalRead(sda);
 raw=PINC & _BV(PC7);
 if(raw==128){
   temp=temp+16;
 }
 clk();
 //raw=digitalRead(sda);
 raw=PINC & _BV(PC7);
 if(raw==128){
  temp=temp+8; 
 }
 clk();
 //raw=digitalRead(sda);
 raw=PINC & _BV(PC7);
 if(raw==128){
   temp=temp+4;
 }
 clk();
 //raw=digitalRead(sda);
 raw=PINC & _BV(PC7);
 if(raw==128){
  temp=temp+2; 
 }
 clk();
 //raw=digitalRead(sda);
 raw=PINC & _BV(PC7);
 if(raw==128){
   temp=temp+1;
 }
 clk();
 
//doing more significant read
/*
0000
.5 1
.25 2
.125 3
.0625 4


*/
//pinMode(sda,OUTPUT);
DDRC|=_BV(DDC7);
//digitalWrite(sda,LOW);
PORTC&=~_BV(DDC7);
clk();
//pinMode(sda,INPUT);
DDRC&=~_BV(DDC7);
//raw=digitalRead(sda);
raw=PINC & _BV(PC7);
if(raw==128){
   tempb=tempb+.5;
 }
clk();
//raw=digitalRead(sda);
raw=PINC & _BV(PC7);
if(raw==128){
   tempb=tempb+.25;
 }
clk();
//raw=digitalRead(sda);
raw=PINC & _BV(PC7);
if(raw==128){
   tempb=tempb+.125;
 }
clk();
//raw=digitalRead(sda);
raw=PINC & _BV(PC7);
if(raw==128){
   tempb=tempb+.0625;
 }
clk();
clk();
clk();
clk();
clk();
clk();
stop1();

if (neg==1){
temp=temp-1;
temp=~(temp);
tempb=(tempb+temp)*-1;
}
else{
tempb=tempb+temp; 
}

}

php code:

<!DOCTYPE html>
<head>
<link rel="stylesheet" type="text/css" href="main.css">
<title>Cpannel</title></head>
<body>
<div id="title">Control Panel</div>
<div id="panel">
<form  method='post'>
<input type='submit' name='button1' value='Read Photo' id="buttona" class="button"/>
<input type='submit' name='button2' value='Turn off' id="buttonb" class="button"/>
<input type='submit' name="button3" value='Read Temp' id="buttonc" class="button"/>
<input type='submit' name="button4" value='Clear' id="buttond" class="button"/>
</form> 
<form  method='post'>
<input type='submit' name='button5' value='Ob1 on' id="buttone" class="button"/>
<input type='submit' name='button6' value='Ob1 off' id="buttonf" class="button"/>
<input type='submit' name="button7" value='Ob2 on' id="buttong" class="button"/>
<input type='submit' name="button8" value='Ob2 off' id="buttonh" class="button"/>
</form> 
</div>
<div class="status">
<br />Status:<br />
</div>
<?php
include "php_serial.class.php"; 
$serial = new phpSerial;
$serial->deviceSet("/dev/ttyUSB0");
$serial->confBaudRate(9600);

date_default_timezone_set("UTC");
if (isset($_POST['button1']))
{
$serial->deviceOpen();
$serial->sendMessage("9");
$read = $serial->readPort();
echo "<div class='status'>" . $read . "</div>";
$serial->deviceClose();
echo "<div class='status'>" . date("h:i:sa") . "</div>";
}
if (isset($_POST['button2']))
{
echo "button2 has been pressed";
}
if (isset($_POST['button3']))
{
$serial->deviceOpen();
$serial->sendMessage("4");
$read = $serial->readPort();
echo "<div class='status'>" . $read . "</div>";
$serial->deviceClose();
echo "<div class='status'>" . date("h:i:sa") . "</div>";
}
if (isset($_POST['button4']))
{
echo "";
}


if (isset($_POST['button5']))
{
$serial->deviceOpen();
$serial->sendMessage("5");
$read = $serial->readPort();
echo "<div class='status'>" . $read . "</div>";
$serial->deviceClose();
echo "<div class='status'>" . date("h:i:sa") . "</div>";
}
if (isset($_POST['button6']))
{
$serial->deviceOpen();
$serial->sendMessage("6");
$read = $serial->readPort();
echo "<div class='status'>" . $read . "</div>";
$serial->deviceClose();
echo "<div class='status'>" . date("h:i:sa") . "</div>";
}
if (isset($_POST['button7']))
{

$serial->deviceOpen();
$serial->sendMessage("7");
$read = $serial->readPort();
echo "<div class='status'>" . $read . "</div>";
$serial->deviceClose();
echo "<div class='status'>" . date("h:i:sa") . "</div>";
}
if (isset($_POST['button8']))
{
$serial->deviceOpen();
$serial->sendMessage("8");
$read = $serial->readPort();
echo "<div class='status'>" . $read . "</div>";
$serial->deviceClose();
echo "<div class='status'>" . date("h:i:sa") . "</div>";
}
?>
</body>

</html>

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