Hello! Using an Xbox One controller (via the wireless USB adapter) with the game causes the crosshairs to constantly jump down to the bottom right once the joystick option is chosen in the game options. It makes it impossible to select the joystick calibration button too. Is there a DOSBox option I can change or something? I'm on Windows 10 64-bit. Thanks!

Ah, here's a solution. See, DOSBOX has a keymapper built into it. A lot of old games aren't exactly sure what to do with all the knobs, buttons and wheels newfangled things have, you at most had 1-3 buttons for a long time.

What you do is, while the game is running, is press control+F1 together. This invokes a keymapper.

From there, you can assign keys to buttons and whatnot.

See if you can edit Dosbox%.conf and make:

[joystick]
timed=false

Usually dosgames have a joystick calibration method, so be sure to calibrate your gamepad within the game as well.
This can be hard to do as gamepads nowadays have round axislimits and the calibration method often wants you to push the sticks into the corners. What I did was to open the Windows gamecontroller panel and select the properties of the gamepad while doing the calibration method, just leave fullscreen for the game (left Alt+Enter) for this so you can see if you get the corners in the properties panel.

Thanks for the suggestion, but all that does is pin the crosshairs towards the the top right instead of bottom right. I can choose the calibration button because the developers oddly forced you to select it using the joystick!

I found a fix for my Xbox One (XInput) controller with Subwar 2050! The default GOG settings work fine without changing them. What you need to do, is run install.exe or config.exe in the game's directory using DOSBox and choose "Reconfigure Hardware Options". Then, when you get to "Control Method", choose "Joystick" using the space bar not enter. Now, hit enter, and it should say "Configuration File Written".

Now, when you start the game, it will ask you to configure the Joystick!

I don't mean to knock you trying, but when this game came out, there wasn't a such thing as analog control save for advanced flight sims.

You either had yaw, pull, and rudder, or a directional pad.