Here are some possible causes of the Steam Deck joystick problem and how to fix them:
Software issue. The system may not be synchronized with the joysticks or may be caused by another program. You can try updating the system.

Physical obstruction. Dirt, crumbs, or dust may be interfering with the joysticks. You can try cleaning them with a cotton swab and rubbing alcohol or a microfiber cloth.

Damage to parts. Joysticks can be damaged, in which case they need to be replaced.

To calibrate the joysticks, you need to:
Click the Steam button, then go to "Settings", then to "Controller".
Open the "Calibration and Advanced Settings" menu.
Select the "Left Joystick Deadzone" option and press the Y button to check the dead zone. If the right joystick is not working, you need to select the "Right Joystick" option and use the R1 button.

If the problem persists,you can seek professional help, such as from Valve's support team.

Thank you so much! I will try these tips.

As for the Calibration you mentioned, I did actually check to see many times.

The right joystick works fine in the calibration part (i.e the cursor moves) but it doesn't seem to register on the SteamOS but works fine when in desktop mode when I move it.

I'm hoping it's just a physical obstruction and no damage to it.