Issue with joypad order when using lr-fbalpha

[BobHarris]

Hi all,
I am considering adding a dedicated controller to my setup for my fighting games in fba (don't know yet which controller).
Ideally I leave this controller hooked up to my Pi and when I start a game in fba it automatically makes this controller the player 1 controller. For all other emulators I use a Dual shock 4.

But there is something strange going on with lr-fbalpha. In port #0 I have my DS4 and in port #1 I have an arcade stick (HRAP 4).
I then changed the joypad order for fba (retropie setup -> configuration/tools -> configedit -> configure basic libretro emulator -> options -> fba -> choose joypad order) and changed the order where the arcade stick is now on top and the DS4 below it.

When I launch for example SF III Third strike the emulator shows that both controllers are recognized (in the bottom left corner), but the DS4 does nothing. I can use the arcade stick and it works fine untill I need a continue. You have to press Start to continue and then suddenly I am controlling player 2 as well with the arcade stick.
Here is a video (I triggered it just by pressing Start in the character select menu):

lr-alpha2012 uses the same config file (/opt/retropie/configs/fba/retroarch.cfg) , but actually works without issues. (Sadly most of my roms only work with lr-fbalpha.) Just to verify this problem is isolated to lr-fbalpha, I also changed the joypad order for psx and that is working fine as well. So only the emulator I need to change gives me these problems.. :')

I updated lr-fbalpha from source but the issue persists.

(When I don't change the joypad order, then both controllers work fine in lr-fbalpha. But then I'd always have to start every fight on the right side of the screen with my fightpad/fightstick.)

Pi Model or other hardware: Pi 3B
Power Supply used: (If using a Pi): Official Pi adapter
RetroPie Version Used : 4.3.5
Built From: Got 4.2 from the Retropie site and updated from there.
USB Devices connected:, Logitech mouse and Microsoft keyboard, Sandisk 128 gb Ultra usb drive
Controller used: Tried several controllers : Xbox 360, DS4, PS1, Hori RAP4