Sorry for late reply. Unfortunately I am not competent enough to make plus_controller_diagnostics.zip or regular v5.6 version of JJ2+ run with WINE manually. Lutris script that automates installation makes use of additional tools some of are AutoHotkey, Helper. Merging and overwriting Lutris installation with your diagnostics tool didn't provide the additional data shown in previous posts.

As I installed JJ2 via WINE manually, JJ2 1.23 without JJ2+ doesn't have phantom controller issues that I experienced with JJ2+ v5.6. Here are my findings;

JJ2 1.23 without JJ2+ (controller is active):
- Characters do not constantly look up.
- Controller buttons work without a problem, they can also be remapped.
- No mouse cursor capture and/or shifting issue occurs.

JJ2 1.23 with JJ2+ v5.6 (controller is active):
- Characters do look up constantly.
- Most of controller buttons do not work. If up button is pressed, character stops looking up, but when you stop pressing, it returns to looking up. Jump, fire, pause, menu buttons work but down, left, right buttons do not work. Buttons cannot be remapped since up button is being constantly pressed. Up button works in menus but other direction keys do not work.
- Mouse cursor moves left in OS level if it is on the window of JJ2. Even if the cursor leaves JJ2 window, it keeps moving to the left edge of the desktop.