| deflection_multiplier_up | normal | 1 |
| deflection_multiplier_down | normal | 1 |
| deflection_multiplier_left | normal | 1 |
| deflection_multiplier_right | normal | 1 |
These are not useable values for the multipliers and it is preventing the joystick from working while in the file selector mode. If you are controlling keys or buttons with the joystick, there are better approaches.
Remove the rows with the joystick preference settings and use something like this:
| kb_left_arrow | greater_than 5 | left |
etc.
Switching to a square dead-zone shape is also a method when controlling buttons from a joystick.
The problem is a joystick is an analog input mixed between two analog axes and a key or button is a 0/100% on/off only output that have no similar work very differently. When using the joystick, we need to clearly separate the outputs from each other in how the input controls them. Without doing that, two keys will always be pressed.
Another thing you could do is to switch the mouse mode in mode 4, so the joystick preferences are not changed, before starting the file selector. The joystick preferences in effect at that time should work OK with the file selector.