Allright I might have made some progress though surprising enough, and that seemed both unrelated to either Saitek or DirectX. While searching for joystick test application, I did find a small application called JoyIDs which purpose is to change the device ids for the joysticks. in the last trials I had the throttle in #1, the joystick in #2 and the rudder pedal in #3. I have previously reinstalled the official drivers too, which was not fixing anything.
Having only the stick not working I changed it's id to #12, not chose really specifically, just wanted to change, and surprisingly enough windows started to see the axis and button in the calibration menu, as well as FSUIPC within FSX.
Not sure at all of what caused this though, but looks fixed, but interesting to keep in my mind. I tried rebooting the PC it worked ,as well as unplugging, rebooting and plugging again and it's still there, I believe I might have solved that issue.