Hello Yurgon,
First, my comment about a new issue was just due to the fact that in seven years, it never happened.
With that said, I do have it working now. It was a combination of things, I don't know which one did the trick or if it was all of them. Here is what I did:
1. repair the install of DCS beta
2. Use JoyId (An old program from back in the day) to change the order of the joystick ports to match the order that DCS displayed from left to right.
3. Downloaded and used the old Thrustmaster Calibration tools. It took three times to get the settings to stick.
Again the weird thing was the whole time the F-18 and F-5 were fine until I used Windows calibration tool. That broke those too. That's when I did the repair install and did the items listed above.