Halp, Makerfarm i3v 8" Printing parts in small sections, Ghost in meh machine?

I was printing test pieces for a part I am designing and all of the sudden it started printing them in small sections at a time. I have googled and searched all over the place for this problem but have ran across no answers.

My machine is a Makerfarm i3v 8" I am using Fusion 360 for design, Meshmixer to package/align and slicer V 0.9.9 Config file: http://pastebin.com/ugVD4vry
Here are some photos of my prints, as you can see the one on the very left is great then it goes down hill from there. The last photo I stopped the print but you can see its printing the skirt wrong but, I haven't changed any setting in slic3r. Any help you guys could provide would be greatly appreciated this problem is driving me nuts ;)

https://drive.google.com/open?id=0B2mmc-lEo2u1Y3JndDdxWG1BcE0
https://drive.google.com/open?id=0B2...zd4VzhaTHZXUW8

~Alec