The USB mode and what outputs buttons or keys are mapped to the digital input, or any input, is not related to the digital input processing in any way. All the digital inputs are handled as a group at the same time, whether they are used or not.
There are about a dozen people using the USB-A digital input function and no one else has reported an issue like this with it. Changing the default USB-A Host mode preference setting from on to off is the only "gotcha". Plugging the adapter in prior to changing that setting and rebooting can cause trouble.
Looking at the default config you are running, the use of the input 3 and/or the left mouse button is inconsistent:
| Mode | | | | |
| 1 | USB A testing | B | normal | digital_in_3 |
| 2 | Mouse | mouse_left_button | normal | digital_in_3 |
| 3 | Scroll | mouse_left_button | normal | digital_in_6 |
| 4 | Bluetooth mouse | mouse_left_button | normal | digital_in_5 |
| 5 | speaker remote | | | |
| 6 | Mouse QS | mouse_left_button | normal | digital_in_5 |
| 7 | Minecraft | mouse_left_button | normal | digital_in_3 |
| 8 | Copy of Minecraft | mouse_left_button | normal | digital_in_6 |
| 9 | FNV | mouse_left_button | normal | digital_in_6 |
| 10 | Battlefield | mouse_left_button | normal | digital_in_3 |
| 11 | Battlefield Vehicle | mouse_left_button | normal | digital_in_6 |
| 12 | Amoured Core | mouse_left_button | normal | digital_in_6 |
| 13 | DBD | mouse_left_button | normal | digital_in_6 |
| 14 | Numbers | | | |
| 15 | Y-N | | | |
| 16 | Arrows | mouse_left_button | normal | digital_in_6 |
| 17 | IR Codes | | | |
It would be easy to lose track of what input is being used between 3, 5 and 6. If 3 is not appearing to work try 5 or 6, see if a different mode is active.
BTW, 16 modes sheets max is the limit. I don't know what happens when that limit is exceeded, even if it is IR codes.