@meleu Hey, thank you for the steps! The problem as described in that other thread certainly sounds like what's happening with me.

This doesn't seem to solve my problem, unfortunately. Something I did notice - in the RetroArch config file, after I set the Bluetooth controller up as Player 2, it still gives me this:

input_player2_b = "nul"
input_player2_b_btn = "nul"
input_player2_b_axis = "nul"
input_player2_y = "nul"
input_player2_y_btn = "nul"
input_player2_y_axis = "nul"
input_player2_select = "nul"
input_player2_select_btn = "nul"
input_player2_select_axis = "nul"
input_player2_start = "nul"
input_player2_start_btn = "nul"
input_player2_start_axis = "nul"
input_player2_up = "nul"

It also still gives me the same problem if I set the Bluetooth controller as player 1 and then manually edit the input_player1_ button variables to represent the buttons on the Bluetooth controller. Nothing changes.

I wonder if a fresh RetroPie install and configuring via RGUI is necessary, like the last guy did. Any thoughts?

The ghost controller is most likely your keyboard. I have the exact same experience here. You could try removing the USB dongle for the keyboard, reboot and see if the PS3 pads are detected as 1 and 2.

It was an issue for me because the PSX emu would not let me play, since the player1 controller was 'occupied', but i got around this by changing some config file, so controller 2 for player 1 and controller 3 is for player 2. Unfortunately i can't remember which config file it was. I am sure that someone would have this on the tip of their tongue.

@Jean

I was actually suggesting that you branch out to other locations on the web, but perhaps having it's own post here may help. However, please keep in mind that if you do not get a reply there that "bumping" or "upping" your posts is not looked kindly upon.