Same code on Windows and Linux, different results

I'm writing a windows dll, but doing some testing of the same code on a linux box.
My function works perfectly on the linux box. Then I copy paste it into Visual Studio, and I copy the datafile that the function works on.

On linux, the code loops over each line of my file, and inputs the data into a vector.
The number of datarows in the vector is 3081, as is the number of lines in my file. Makes sense.

However, when compiled as a dll and executed under windows however, I get to datarows in my vector, for each line in my datafile.

Expected output from both functions would be
3081
3081

Linux/GCC 3.4.6 output is
3081
3081

Windows/Visual Studio/Discipulus(the app that calls my dll) output is:
3081
6162 (aka 3081 * 2)

I'm attaching the code below, hoping that someone can see wtf is going on.
Or tell me that vectors work differently on Windows than on Linux, or something similar, so I can figure this out. I've programmed a lot, but I'm somewhat new to C++

//Code on windows, Visual Studio Pro 2008
ifstream myfile ("c:\\training.txt", ios::in);
if (myfile.is_open()) {
	int counter = 0;
	int params = 0;
	string line;
	while (!myfile.eof()) {
		getline (myfile,line);
		if(line.length() == 0) break;
		vector<string> dataRow;
		params = explode(line, "    ", dataRow);
			for(int i = 0; i < NR_OF_INPUTS; i++) {
			logfile << i << endl;
			inputVector[i].push_back(StrToF(dataRow[i]));
		}
		
		counter++;
	}
	myfile.close();
	logfile << counter << endl;
	logfile << inputVector[0].size() << endl;
}
 
//Code on linux. Vim + GCC 3.4.6
ifstream myfile ("training.txt", ios::in);
if (myfile.is_open()) {
   int counter = 0;
   int params = 0;
   string line;
   while (!myfile.eof()) {
      getline (myfile,line);
      if(line.length() == 0) break;
      vector<string> dataRow;
      params = explode(line, "    ", dataRow);
       if(dataRow.size() != NR_OF_INPUTS) cout << "fel" << endl;
       for(int i = 0; i < NR_OF_INPUTS; i++) {
         logfile << i << endl;
          inputVector[i].push_back(StrToF(dataRow[i]));
       }
        counter++;
   }
   myfile.close();
   cout << counter << endl;
   cout << inputVector[0].size() << endl;
}

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