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The code has lots of bugs in it. I found them by adding lots of println statements that displayed the values of many of the program's variables as the code executed.
I changed:

final int...

Some more suggestions for testing:
Have the output files be small enough that it can easily be visually verified. 32K is too big
Have a max of 30 lines.
Add a toString() method to the Student...

There should only be one definition for the Scanner object. For easy testing it should contain all the responses that will be read in the program when the next methods are called.
Can you merge all...

For easier testing, define the Scanner object with the needed input for testing instead of requiring the tester to type in data. For example:

Scanner input = new Scanner("the input...

I found my error. A previous question had a class named: Files that was being picked up. Renamed it out of the way and now both classes you posted compile without errors.

How do I test the...

I just downloaded the java 1.7 SDK two days ago.

I can't compile the code for testing because of the errors I posted. I am using the javac command that comes with the SDK for java 1.7 to compile the code.

I have no idea what compiler JGrasp...

Problem fixed, see below.

Could you post a copy of the input file for testing?