This is still an issue. I use wired mayflash arcade sticks and when used in conjunction with an 8Bitdo controller the emulators always randomly exit. The ps3 bluetooth driver package was never installed. I use 4 of these arcade sticks and unplugging all of them every time i want to play a game with a pad is not an optimal solution.

(decent budget sticks btw, they accept sanwa parts and are like $54 on amazon)
http://www.mayflash.com/Products/XBOXXBOX360/MF002.html

Hello,

I had to reinstall mame2003 in the end for the settings to work. I have lost my controls though. I run a game hit tab and choose "input (general" and try and configure P1 and P2 etc but my bartop buttons are not detected now.

They work fine in ES and all other emulators execpt this arcade/mame2003 emulator.

Any ideas what it might be?

You could edit the shader file directly
https://retropie.org.uk/forum/topic/2592/video-smoothing-yay-or-nay/26