Loop Improperly Executing with Array

[Winged Glyph]

I'm trying to recreate a basic student database and having trouble with the second half. It works the same whether or not I incorporate the first half, so I just appended the second portion below.
I can run the code just fine, but when it asks for the user to input 1 or 0, at the end, and I input it either one, the code will output the course previously entered, skip about four lines, and wait for the "cin >> stop;".

The BIOLOGYCOURSES file follows this format:

CC100
HP101
EN101
EN102
EN200
EN201

and so on.

Student_Transcript_Data is like this:

1067878
CS150
B
FA2014
1067878
RL101
C
SP2014
1067878
PH223
B
FA2014

**********************************************************

#include <iostream>
#include <string>
#include <sstream>
#include <istream>
#include <fstream>
#include <iomanip>

using namespace std;
int stop;

int main()
{

	const int MAX_Students = 6;
	bool CanTake = false;
	int RegistrationFinish = 0;
	int CourseDecrement = 3;

	ifstream inFile;
	ofstream outFile;
	ofstream NextSemester;
	ifstream BiologyCourses;
	ifstream CoursesTaken;

	string ChosenCourses[7];
	string CourseToTake;
	string BiologyArray[50];
	string RegistrationFinishString;
	string course;
	string StudentIDString;
	string StudentID;
	string CourseInput;

	
	BiologyCourses.open("E:/College Work/Intermediate Programming/BIOLOGYCOURSES.txt");
	NextSemester.open("E:/College Work/Intermediate Programming/Next_Semester.txt");
	CoursesTaken.open("E:/College Work/Intermediate Programming/Student_Transcript_Data.txt");


	struct CompletedCourses
	{
		string StudentID;
		string CourseID;
		string Grade;
		string DateTaken;
	};

	int index = 0;

	CompletedCourses CompletedCoursesArray[35];

	while (BiologyCourses)
		{
				getline (BiologyCourses, course);
				BiologyArray[index] = course;
				index++;
		}
	index = 0;

	while (CoursesTaken)
		{
				getline (CoursesTaken, CompletedCoursesArray[index].StudentID);
				getline (CoursesTaken, CompletedCoursesArray[index].CourseID);
				getline (CoursesTaken, CompletedCoursesArray[index].Grade);
				getline (CoursesTaken, CompletedCoursesArray[index].DateTaken);
				index++;
		}	
	index = 0;

	
	while (RegistrationFinish != 1)
	{
		CanTake = false;
		cout << "Enter the course you want to take." << endl;
		getline(cin, CourseToTake);
		cout << "Please enter your student ID." << endl;
		getline (cin, StudentID);
		stringstream(StudentIDString) >> StudentID;
		

		
			if (BiologyArray[index] == CourseToTake)
			{
				cout << endl << "You may take " << CourseToTake << "." << endl;
				
			if ((StudentID == CompletedCoursesArray[index].StudentID) && (CourseToTake == CompletedCoursesArray[index].CourseID))
			{
				cout << "You have already taken this course and made a(n) " << CompletedCoursesArray[index].Grade << "." << endl;
			}
				ChosenCourses[CourseDecrement] = CourseToTake;
				CanTake = true;
				CourseDecrement--;
				index++;
			}
		index = 0;

	if (CanTake == false)
		{
			cout << endl << "You may not take this course(s)." << endl;
		}
		
	if (CourseDecrement > 0)
		{
			cout << endl << "You may register " << CourseDecrement << " more course(s)." << endl;
			cout << endl << "Enter 1 if you are finished. Enter 0 to continue to add courses." << endl;
			getline (cin, RegistrationFinishString);
			stringstream(RegistrationFinishString) >> RegistrationFinish;
		}

	if (CourseDecrement == 0)
		{
			cout << endl << "All course slots have been filled." << endl;
			RegistrationFinish = 1;
		}													
	
	for (int index = 3; index >= 0; index--)
		{
			cout << ChosenCourses[index] << endl;
		}
	}

	
		NextSemester.close();
		CoursesTaken.close();
		BiologyCourses.close();

	cin >> stop;
	return 0;
}