Coming from someone who just completed a 2 year grad program last may...and nearly lost his mind on a monthly basis due to stress, commitments, and hell....
Well, my thoughts:
It was incredibly stressful, and, while I can't speak for your girlfriend, I can say that I regularly went back and forth on my relationship at the time (also long distance, and 2+ years)... One day, I'd be grateful for the support, and the next angry that I couldn't see him/touch him/having him physically be there. I'd be happy that someone cared about me and would check in, and then i'd be annoyed and think that i was wasting his time and not giving him what i felt he wanted/deserved.
Now, I share this because I'm trying to illustrate the following point:
A stressful grad program can leave you fucking nuts and really unable to properly balance and take care of yourself and your emotions.
My two cents:
Be there, and go with the flow. If she needs a break, support that. If she wants it continue, support that. Help her out, even if you're just there as a friend...hell, friends got me through some rough deadlines and busy periods those 2 years....
But, if long distance and this back-and-forth-ness don't work for you...well, you have needs that deserve to be recognized as well.
Regardless of what happens, best of luck...