clearTimeout and WARNING: Out of memory while appending to array

Could it be that Start_GPS is getting called twice, so is then overwriting the value from SearchDuration? In code that I write I tend to explicitly check and clear the interval before I set it.

Also, I'd try and call require('GPS').connect only once - as otherwise every hour it'll add another GPS handler and will probably run out of memory - even if you set gps to "", the handler will still be receiving data from Serial4.

Just a quick JS thing too - if you say var gps in a function, that'll create a local variable rather than using a global one. So for example if you write var gps = ...; in a function, when you leave the function the reference to gps will be lost (although it'll still keep working).

Maybe try:

Serial4.setup(9600,{tx:C10,rx:C11});
var SleepDuration = null;
var SearchDuration = null;
var foundFix = 0;
var gps = undefined;

function Start_GPS(){
  
  console.log("Starting GPS...");
  //Reset fix found
  foundFix=0;
  
  //After 120 seconds disable the GPS regardless
  if (SearchDuration) clearTimeout(SearchDuration);
  SearchDuration = setTimeout(function (e) { SearchDuration=undefined; Stop_GPS(); }, 60000);
 
  //Set enable pin mode
  pinMode(A9,'output');
  
  //Set enable pin to high
  digitalWrite(A9,1);
}

function Stop_GPS(){
  if (SearchDuration) {
    clearTimeout(SearchDuration);
    SearchDuration = undefined;
  }
  digitalWrite(A9,0);
  console.log("Disabling GPS...");
}

function onInit(){
  //load gps
    gps = require("GPS").connect(Serial4, function(data) {
    console.log(data);
    //Check if we have a fix
      if(data.fix>0)
      {
        console.log("Send SMS:" + data.lat + "|" + data.lon);
        foundFix=1;
        Stop_GPS();
      }
  });
console.log("Starting up device & Setting timers...");
setInterval(function (e) { Start_GPS(); }, 360000);
Start_GPS();
}
onInit();