After doing a bunch of random stuff I give up. I'm 99% sure at this point you can't assign individual roms different values from mupen64plus.cfg [Video - Rice]

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.

N64 doesn't flawlessly work on the Pi. Overclocking a little does help, but some games will always have lag, some unplayable. It's a shame but I think until we see a Pi 4, this will always be the issue.