I experience the same problem and did all the trouble shooting that the group has done. I found the problem. It has nothing to do with the hardware, the cables or a bug in the software. I found out what was wrong by accident. I noticed that when I moved windows off the simulator to another screen i.e. VFR Map, I would loose my control of the HOTAS and the Rudder. When I clicked back on the simulator screen the control returned. Simply if you click on any other screen or window such as starting a timer for VFR flight YOU MUST CLICK BACK INTO THE SIMULATOR OR THE FLIGHT CONTROLS BECOME INACTIVE.