So, here is the first layer of a print I was attempting on software version 8.3:
http://i.imgur.com/yKhgfMg.jpg

Here is the first layer of that SAME file on software 1.3.1:
http://i.imgur.com/YTCQzFQ.jpg

And this seems to happen on any 10.X version software and above, including the current "stable" 1.2.1. I cannot print a THING if I upgrade past 8.3.

Just to test it, I downgraded back to 8.3, making sure to keep my same calibration and bed-leveling settings, and it printed like that first picture again. I even tried the 8.3 software with the newer firmware that came with 1.3.1 to see if it was the firmware or PC application, and it printed the same as before on 8.3, so it's not the firmware.

I think the new software just goes too damn fast. I noticed that on the old software, it estimates the part will take nearly 10 hours to print... while on the new software it estimates 7 hours. The extruder also looks like it's moving faster when I was on 1.3.1 as well.

I have been having many issues with the rafts in 8.3, as well as have been trying to use external slicers, so being stuck on 8.3 is a huge problem for me, but upgrading above it makes my printer completely useless. I want to use the features that were added in newer versions of the software already, especially the ability to use an external slicer and disable the wave bonding in the internal one. But I can't use anything above 8.3 if my printouts come out like that.