If anyone else has this problem, it seems that InputAutoCfg.ini is what you are supposed to edit. Changing plugged to false just gave a no controller message. Since I didnt see any section for order, I changed the order of the controller configs but that didnt change anything. However just deleting the nes gamepad section worked and now my bluetooth controller is controller 1. It also stayed that way through restarting.
@mankysteve I'm not sure where you read that but as an experiment I tried "Star Wars - Rogue Squadron (USA) (Rev A).n64" It runs with a lot of audio glitches and slowdown. I would not call it playable. I am using a Pi3 at stock settings and mupen64plus tested with all of the various plugins.
If you are determined to play it just mess around with the resolution and plug-ins using runcommand menu and see what feels best to you.
I've also noticed a problem with blending while I was helping to troubleshoot recent issues with missing textures, but I wasn't certain that the blending issue was an existing problem or something new, as I rarely test N64 emulation.
If you're familiar with editing files via SSH, you can edit /opt/retropie/emulators/mupen64plus/bin/mupen64plus.sh and try removing zelda from that blacklist to see if the problem is resolved. I'll take a look when I have some free time.
I've figured it out, after clean reinstalling Retropie all is working fine.
When I go to Retropie Setup and only update mupen64plus via core/main packages (didn't remeber the exactly one) the same issue comes back.
Anyone has an idea ?
Update: Ok i keep it up testing and there is one more thing.
If i did'nt update all works fine. After that i manual edited the mupen64plus.sh to that one which is used after updated mupen64plus package. From here the issue comes back again.
So it seems, there is a bug in the new mupen64plus.sh handeling the texture packages.
@dankcushions it's quite playable, although the sound isn't 100% correct, some minor artifacts as well. I did an update via source when I got the email it had released, and a binary just now which didn't seem to do anything more, so I wonder if it's worth doing another update from source. Hi-res works just as well as the normal emulator so that's most definitely the way to go)
I'll have to have a go on my Ubuntu build as well and see how that plays.
Good to see the ongoing support potential in your other post, I'll do that one once payday comes around, brassic this week:(