I ran the FSX in Full Screen mode and I don't have the issue. I followed all of the instructions about turning off power management for the USB ports but to no avail.
I changed the view to full screen under View menu in FSX. Then I went out and alt+tab to get to the www.simroutes.com page which usually causes the FSX to lose the controller when I am in Windowed mode.
I alt tabbed out about 3-5 times.
I wasn't having any issues now with the controller/yoke disappearing.