It appears that I solved this problem. However, I don't understand how.
The only files that were running choppy were files shot on the c300 (XF files).
I downloaded the new ama link for it and it appears that I have solved the issue. I just don't understand why it worked. All the files I was running were consolidated into the preferred .mxf files that Avid loves so dearly.
Why would the ama link update for canon fix such a thing? Weren't those files converted and no longer being referenced via ama link?