COM PORT PROBLEM (Have read trouble shooting guide)

I have properly installed my arduino drivers, and in the ide have selected the proper ports and arduino board.

my problem however, is that with the current program I am attempting to upload (it has successfully compiled) I am getting the error
"Serial Port COM ___" already in use. I would typically associate this with a bus contention problem, but when the issue starts I often have trouble getting blink to load, which uses no serial interfacing.

If it helps, my code is posted below. It is for a gps/compass datalogger. The board is an arduino uno r3. Any advice that is given is much appreciated!

/*load the Hart Libraries, and Arduino libraries for reading the compass, GPS, and for data logging. 
Note some of this code was taken from the public domain, and some portions were taken from the jeremy Blum
and Element 14 tutorials*/
#include <NewSoftSerial.h>
#include <TinyGPS.h>
#include <SD.h>
#include <Wire.h>
#include <stdlib.h>

int HMC6352Address = 0x42;
int slaveAddress;
byte headingData[2];
int i, headingValue;

NewSoftSerial nss(6,255);
TinyGPS gps;
static char dtostrfbuffer[20];
int CS = 8;
int LED = 13;

//Define String
String SD_date_time = "invalid";
String SD_lat = "invalid";
String SD_lon = "invalid";
String dataString ="";

static void gpsdump(TinyGPS &gps);
static bool feedgps();
static void print_float(float val, float invalid, int len, int prec, int SD_val);
static void print_int(unsigned long val, unsigned long invalid, int len);
static void print_date(TinyGPS &gps);
static void print_str(const char *str, int len);

void setup()
{
  slaveAddress = HMC6352Address >> 1;
  pinMode(CS, OUTPUT);  //Chip Select Pin for the SD Card
  pinMode(LED, OUTPUT);

  //Serial interfaces
  Serial.begin(9600);
  nss.begin(4800);
  
  //Connect to the SD Card
  if(!SD.begin(CS))
  {
    Serial.println("Card Failure");
    return;
  }
  
  
  Serial.print("Testing TinyGPS library v. "); Serial.println(TinyGPS::library_version());
  Serial.println("by Mikal Hart");
  Serial.println();
  Serial.print("Sizeof(gpsobject) = "); Serial.println(sizeof(TinyGPS));
  Serial.println();
  Serial.println("Sats HDOP Latitude Longitude Fix  Date       Time       Date Alt     Course Speed Card  Distance Course Card  Chars Sentences Checksum");
  Serial.println("          (deg)    (deg)     Age                        Age  (m)     --- from GPS ----  ---- to London  ----  RX    RX        Fail");
  Serial.println("--------------------------------------------------------------------------------------------------------------------------------------");
}

void loop()
{
  bool newdata = false;
  unsigned long start = millis();
  Wire.beginTransmission(slaveAddress);
  Wire.send("A");
  Wire.endTransmission();
  delay(500);
  Wire.requestFrom(slaveAddress,2);
  i=0;
  while(Wire.available() && i < 2)
  {
    headingData[i] = Wire.receive();
    i++;
  }
  headingValue=headingData[0]*256+headingData[1];
  // Every second we print an update
  while (millis() - start < 1000)
  {
    if (feedgps())
      newdata = true;
  }
  
  gpsdump(gps);
  int dat = headingValue/10;
  int vap= headingValue % 10;
  
  //Write the newest information to the SD Card
  dataString = SD_date_time + "," + SD_lat + "," + SD_lon + ","+" "+dat+"."+vap+"degrees";
  if(SD_date_time != "invalid")
    digitalWrite(LED, HIGH);
  else
    digitalWrite(LED, LOW);
    
  //Open the Data CSV File
  File dataFile = SD.open("LOG.csv", FILE_WRITE);
  if (dataFile)
  {
    dataFile.println(dataString);
    Serial.println(dataString);
    dataFile.close();
  }
  else
  {
    Serial.println("\nCouldn't open the log file!");
  }
}

static void gpsdump(TinyGPS &gps)
{
  float flat, flon;
  unsigned long age, date, time, chars = 0;
  unsigned short sentences = 0, failed = 0;
  static const float LONDON_LAT = 51.508131, LONDON_LON = -0.128002;
  
  print_int(gps.satellites(), TinyGPS::GPS_INVALID_SATELLITES, 5);
  print_int(gps.hdop(), TinyGPS::GPS_INVALID_HDOP, 5);
  gps.f_get_position(&flat, &flon, &age); 
  print_float(flat, TinyGPS::GPS_INVALID_F_ANGLE, 9, 5, 1); //LATITUDE
  print_float(flon, TinyGPS::GPS_INVALID_F_ANGLE, 10, 5, 2); //LONGITUDE
  print_int(age, TinyGPS::GPS_INVALID_AGE, 5);

  print_date(gps); //DATE AND TIME

  print_float(gps.f_altitude(), TinyGPS::GPS_INVALID_F_ALTITUDE, 8, 2, 0);
  print_float(gps.f_course(), TinyGPS::GPS_INVALID_F_ANGLE, 7, 2, 0);
  print_float(gps.f_speed_kmph(), TinyGPS::GPS_INVALID_F_SPEED, 6, 2, 0);
  print_str(gps.f_course() == TinyGPS::GPS_INVALID_F_ANGLE ? "*** " : TinyGPS::cardinal(gps.f_course()), 6);
  print_int(flat == TinyGPS::GPS_INVALID_F_ANGLE ? 0UL : (unsigned long)TinyGPS::distance_between(flat, flon, LONDON_LAT, LONDON_LON) / 1000, 0xFFFFFFFF, 9);
  print_float(flat == TinyGPS::GPS_INVALID_F_ANGLE ? 0.0 : TinyGPS::course_to(flat, flon, 51.508131, -0.128002), TinyGPS::GPS_INVALID_F_ANGLE, 7, 2, 0);
  print_str(flat == TinyGPS::GPS_INVALID_F_ANGLE ? "*** " : TinyGPS::cardinal(TinyGPS::course_to(flat, flon, LONDON_LAT, LONDON_LON)), 6);

  gps.stats(&chars, &sentences, &failed);
  print_int(chars, 0xFFFFFFFF, 6);
  print_int(sentences, 0xFFFFFFFF, 10);
  print_int(failed, 0xFFFFFFFF, 9);
  Serial.println();
}

static void print_int(unsigned long val, unsigned long invalid, int len)
{
  char sz[32];
  if (val == invalid)
    strcpy(sz, "*******");
  else
    sprintf(sz, "%ld", val);
  sz[len] = 0;
  for (int i=strlen(sz); i<len; ++i)
    sz[i] = ' ';
  if (len > 0) 
    sz[len-1] = ' ';
  Serial.print(sz);
  feedgps();
}

static void print_float(float val, float invalid, int len, int prec, int SD_val)
{
  char sz[32];
  if (val == invalid)
  {
    strcpy(sz, "*******");
    sz[len] = 0;
        if (len > 0) 
          sz[len-1] = ' ';
    for (int i=7; i<len; ++i)
        sz[i] = ' ';
    Serial.print(sz);
    if(SD_val == 1) SD_lat = sz;
    else if(SD_val == 2) SD_lon = sz;
  }
  else
  {
    Serial.print(val, prec);
    if (SD_val == 1) SD_lat = dtostrf(val,10,5,dtostrfbuffer);
    else if (SD_val == 2) SD_lon = dtostrf(val,10,5,dtostrfbuffer);
    int vi = abs((int)val);
    int flen = prec + (val < 0.0 ? 2 : 1);
    flen += vi >= 1000 ? 4 : vi >= 100 ? 3 : vi >= 10 ? 2 : 1;
    for (int i=flen; i<len; ++i)
      Serial.print(" ");
  }
  feedgps();
}

static void print_date(TinyGPS &gps)
{
  int year;
  byte month, day, hour, minute, second, hundredths;
  unsigned long age;
  gps.crack_datetime(&year, &month, &day, &hour, &minute, &second, &hundredths, &age);
  if (age == TinyGPS::GPS_INVALID_AGE)
  {
    Serial.print("*******    *******    ");
    SD_date_time = "invalid";
  }
  else
  {
    char sz[32];
    sprintf(sz, "%02d/%02d/%02d %02d:%02d:%02d   ",
        month, day, year, hour, minute, second);
    Serial.print(sz);
    SD_date_time = sz;
  }
  print_int(age, TinyGPS::GPS_INVALID_AGE, 5);
  feedgps();
}

static void print_str(const char *str, int len)
{
  int slen = strlen(str);
  for (int i=0; i<len; ++i)
    Serial.print(i<slen ? str[i] : ' ');
  feedgps();
}

static bool feedgps()
{
  while (nss.available())
  {
    if (gps.encode(nss.read()))
      return true;
  }
  return false;
}

Which COM port are you using for the Arduino?

it depends on the arduino. for the arduino set up on com port 10, I use com port 10. For the arduino on com port 6, I use com port 6, and for the arduino set up on com port 9, I use com port 9

It seems that I have this problem quite often when I use serial interfaces, but when I stop using them, the problem persists

also, I go to devices ->"ports com and lpt" my computer recognizes that the arduino is on the given port even though i get that error message when i attempt to upload a program

I just tried to get multiple Arduinos on a USB Hub and I get the same serial open error with the Arduino IDE. I tried Terraterm and it seems to handle multiple com ports better, but it got hung up once. I am wondering if you interface with only one Arduino and then have TTL serial communications or I2C setup would be better for the application you describe.