To save yourself the trouble on subsequent launches you might want to set it as start up profile.

Save the profile and switch to it by clicking the X52 icon in tray and selecting the name of the profile you've just created. Unless you intend to modify axis curves or something really special you wont need anything to use that stick with ED. This small companion app to the game Elite Dangerous automatically controls the button lights on your Saitek X52 Pro joystick so that they reflect the current state of your ship or SRV in the game. You might also want to clear the assignments for the scroll wheel and mouse fire the same way you did with the wheel button. What do you need them for Elite Dangerous supports that stick out of the box. Also remove the shift button for the remaining shift state by clicking the blue icon below the mode name. You go into the game and into the mappings, then set your buttons there. If you don't use the SST for Elite Dangerous I suggest you also remove all the shift state columns save for the first one by clicking the 'x' icon next to each mode name. There are two ways to bind your stick to elite: 1: direct mapping.

The button will now work normally in game To fix this problem you have to create a new profile in SST (the default profile uses this button to emulate right mouse button) by clicking the X52 icon in your tray and selecting 'profile editor', then scroll down to 'wheel button' and switch it to 'unprogrammed' by clicking the arrow to the right of button name and selecting appropriate option.

Don't listen to people telling you to uninstall drivers.

Elite dangerous bindings saitek x52 pro