Ok turns out I accidentally posted that screenshot whike running code that had the reverseSensor() implemented, I knew that they were in-phase but I wanted to see what that function did on a whim and forgot I was running that version of the code. Another thing I realized was that I was setting the desired pid value to 1000 (a mentor and I didn't know that the encoder values are scaled) and so the whole time I was trying to run my code the robot was trying to reach an insanely high encoder value.
Thanks for all your help, we just need to figure out how the scaling works now.
Also, this is the code I was running, what I linked earlier was an archive of my projects (which you might have realized included this project)
https://drive.google.com/file/d/0B32...ew?usp=sharing