Updated and now failing

[techcoast 0]

I updated my custom machine to the latest firmware and also cura to the latest. Now, I get horrible under extrusions. Mainly when I turn on supports, but a little without as well. Everythin is calibrated, and I've tried even starting over on a new profile for the filament. I'm running PLA at 200c. Adhesion is great and the machine seems to move just fine. I just can't , for the life of me, figure out where the failure is occurring.  The attached pics show what I'm talking about. The first one I printed the robot with no real issues, I tried my own stl without support and it was okay but the smaller features failed (On top). I tried the exact same file again with tree supports and you can see the results. I tried a different file later with the holes on the side and I noticed that I was getting under-extrusion where the nozzle starts back up again after the hole. Thoughts?!