I have spent the previous 2 years of my 3 year phd program attempting to replicate the results of a previous student in the lab (who was recently awarded her phd for the work). After trying to reproduce her results using her method, using different methods and even going so far as to generate a new transgenic cell line, I CANNOT REPRODUCE any of her results.
Should I include these negative results in my thesis? Has anyone experienced a similar situation before?

I've not experienced a similar situation myself although I'm aware of people who have. The answer is quite clearly yes. If your results have been obtained through good experimentation then they need to see the light of day. No question. We have to be honest and we can't bury anything that doesn't confirm what has been found previously. We need to be open and talk about why they don't confirm what was found previously.

The point is that you're not 'disproving' anything, because nothing is really 'proved'. You have found different results - you need to explain why. She could be wrong, you could be, you both could be.