I'm using Windows 8.1 and a Saitek X45. I had an issue where the joystick would show in the controllers list while at the main menu but once I get into the game, the joystick disappears from the controllers list.
I am able to get the joystick to show up in the controllers list during gameplay and work by leaving the Windows game controllers window open. Go to Devices and Printers > Right-Click your joystick > Select "Game controller settings". A list of controllers connected to your computer should show up. Leave this("Game controller settings") window open.
Let me know if this worked for anyone else.