I have commented the problem into the code below. See the Store2 vector in the Write Data function. I get error 0xC0000005: Access Violation with no warnings. Any help figuring out why would be appreciated.

#include <iostream>
#include <fstream>
#include <string>
#include <sstream>
#include <vector>
#include <stdlib.h>
using namespace std ;

struct Weather
{
    int winddr;
    double windsp;
    double ETTsea;
	double Hsea;
    double VMDsea;
    double ETTswell;
	double Hswell;
	double VMDswell;
	double Hs;
};

struct Found {
    double height;
	double degrees;
	double prob;
	double count;
};

struct Found2 {
    double height;
	double VMDsea;
	double VMDswell;
	int yes;
};

//-----------------------------------------------------------------------------------------------------------------------------
void Write_Data(vector <Weather> Data) {
  
  double count, y, z, angle1, angle2, count2;  
  int x, a, b;
  Found Temp;
  Found2 Temp2;
  vector <Found> Store;
  vector <Found2> Store2;
  
  count2 =0;
  
    for (b=0; a<Data.size(); a++) {
      Temp2.height =0;
	  Temp2.VMDsea =0;
	  Temp2.VMDswell =0;
	  Temp2.yes=0;
	  Store2.push_back(Temp2);
	}//for statement
  
  
  for (y=0; y<=20.0; y = y+.5) {
	 if (angle1=0 && Data[x].Hs <= y)
	    count2 = count2+1;
		  
	Temp.count = count2;
	Temp.degrees = 0;
	Temp.height = y;
	Temp.prob = count2/105192.0;
	count2 = 0;
	Store.push_back(Temp);
	  for (z=15; z<=180.0; z = z + 15.0) {
		  count =0;
		  for (x=0; x<Data.size(); x++) {	  
			angle1 = abs(Data[x].VMDsea - Data[x].VMDswell);
			angle2 = abs(360-angle1);
			if (angle1>180.0) {
				angle1=angle2;
			} //for if
			if (angle1> z-15 && angle1 <=z && Data[x].Hs <= y) {
	     		count = count +1;
                if (y==20) {
			Temp2.height =Data[x].Hs;
			Temp2.VMDsea =Data[x].VMDsea;
		                Temp2.VMDswell =Data[x].VMDswell;
			Temp2.yes=1;
     //THIS IS WHERE PROGRAM ERRORS WITH 0xC0000005: Access Violation
                                                Store2[x] = Temp2;
				} //for if
			} //for if
		  }  //for x
		    Temp.count = count;
			Temp.degrees = z;
			Temp.height = y;
			Temp.prob = count/105192.0;
			Store.push_back(Temp);
			count=0;
		}  //for z
  cout<<y<<endl;
  }  //for y


  ofstream DataFile("results.txt");
  cout<<"Writing...Please wait...."<<endl;
  for (a=0; a<Store.size(); a++)  {
     DataFile << Store[a].height <<" "<< Store[a].degrees <<" "<< Store[a].prob <<" "<<Store[a].count<<endl; 
	 cout<<a/Store.size()<<endl;
  }
  ofstream DataFile2("results2.txt");
  cout<<"Writing...Please wait...."<<endl;
  for (b=0; b<Store.size(); b++)  {
     DataFile2 << Store2[b].height <<" "<< Store2[b].VMDsea <<" "<< Store2[b].VMDswell <<" "<<Store2[b].yes<<endl; 
  }
 
}  //for function

//-----------------------------------------------------------------------------------------------------------------------------
vector <Weather> Load_Data() {
  string DataStream1;
  vector<Weather> Data;

  cout<<"Pulling in data...Please wait...."<<endl;


 //Load First Data File
  ifstream DataFile1("GROW.txt");
  while(getline(DataFile1, DataStream1))
  {
	  istringstream Incoming(DataStream1);
      Weather w;
      Incoming >> w.winddr >>w.windsp >>w.ETTsea >> w.Hsea >> w.VMDsea >> w.ETTswell >> w.Hswell>> w.VMDswell >> w.Hs;
      Data.push_back(w);
  }

  //Load Successful
  cout<<"Load successful..."<<endl;
  cout<<"Array size "<<Data.size()<<endl;
  return Data;
}

//-----------------------------------------------------------------------------------------------------------------------------
int main()
{
  //Declare variables
  vector<Weather> Data;
  //Call the functions
    Data = Load_Data();
	Write_Data(Data);
return 0;
}

The value of 'x' is invalid subscript at the point where the error occurs, it exceeds the size of Store2.

You are using uninitialized variables (x, a) there, it's a bad practice.

void Write_Data(vector <Weather> Data) {
  
  double count, y, z, angle1, angle2, count2;  
  int x, a, b; 
[B]  // what might be the value of 'a' at this point?[/B]
  cout << "a is initially: " << a << '\n';

  Found Temp;
  Found2 Temp2;
  vector <Found> Store;
  vector <Found2> Store2;
  
  count2 =0;
  
    for (b=0; a<Data.size(); a++) {
      Temp2.height =0;
	  Temp2.VMDsea =0;
	  Temp2.VMDswell =0;
	  Temp2.yes=0;
	  Store2.push_back(Temp2);
	}//for statement

 [B]   // how many entries were added to Store2 ...[/B]
    cout << "Store2 size: " << Store2.size() << '\n';
...

Then you have ...

if (angle1=0 && Data[x].Hs <= y)
	    count2 = count2+1;

Did you mean comparison instead?

if (angle1==0 && Data[x].Hs <= y)
	    count2 = count2+1;

Note that in Data[x].Hs above, x is also uninitialized but doesn't trigger any error due to the malformed if condition ...

So revise your code and check how it behaves after that ...