The best way to deal with this is to go over ALL their heads.
Write a very polite letter to your senior senator, and make the subject of the letter something like REQUEST FOR ASSISTANCE WITH A VETERAN'S ADMINISTRATION ISSUE--as the VA has been in the news, your business will go to the top of the pile.
Explain everything you've explained here, make it as clear and as brief as possible, and provide, in addition to your address, your phone number(s) where you can be reached. Then provide, as enclosures, copies of all the documentation you can get your hands on. If you have the names of the people you spoke with on the phone, be sure to NAME NAMES. If it's too difficult to put all that in the letter, try writing out your recollections of the conversation(s) and make that an enclosure to your letter. Make sure your letter is typed, try to keep the main points on one page, if possible, and fill in the details with the enclosures. Sign it Very Respectfully -- they always love that military bearing.
Here is what will happen to your letter--it will be SHOT over to the OLA (Office of Legislative Affairs), put on a tickler, and someone from OLA will RIDE the VA until they resolve these issues. Then, your senior senator will write you a letter back when it's all settled.
Understand that everything you write will be xeroxed by your Senator's office and sent to OLA, and xeroxed by OLA and sent over to the VA. Someone at VA HQ will be calling the people with whom you spoke and they'll be riding them like a tired hoss.
Now, will you win? Not sure--I seem to remember getting a D kind of knocked you off the rails--if you got more than one D, that could have impacted an entire semester or more, but I just don't remember so I can't really tell you. The larger point here, though, is that you are getting two sets of guidelines and one says "YOU OWE" and the other says "YOU DON'T OWE" and that needs to be resolved.
Please come back and let us know how you make out with this.