I found the issue, it was my rudder pedals. The toe presses were being mapped to aircraft control in the Axis Assign screen. When I was inputting rudder commands and pressing the toe in some, the aircraft went into some unexpected maneuvers. This causing me to try to correct my flight and then everything rolling into a big FUBAR.
I cleared the Axis Assign for my peddle and mapped the Rudder and Toe brakes for what they are supposed to do. I haven't had the problem since, I have to do this for each of my modules.
Strange the game would map toe presses to regular flight controls.
I am using a Logitech/Saitek Pro Flight Rudders and an x52 Pro HOTAS.