Go to the tab in x360ce and select the offending thumbstick.
The 4.x Alpha release brought several essential upgrades for users: x360ce 41000 alpha fixed
The build bridges the gap between old-school hardware compatibility and modern operating system security. While stable releases of the older 3.x architecture are fine for retro games emulation, this virtual-driver approach is strictly mandatory for modern AAA gaming. Go to the tab in x360ce and select the offending thumbstick