So i did some more testing and have the following results.
All emulators on the SNES side are having this issue.
I tried the NES emulator and that works fine with 2 players.
The only difference i could see between the Rpi1 and Rpi2-3 image is that for the 2-3 lr-snes9x-next is used and on the Rpi1 the snes9x is used. Also the snes9x is not working on the Rpi1.
So i have the following questions. Why has the Rpi2-3 image the other emulator installed and how can i install this on the Rpi1? I tried it with Sudo Make and Make Install but it failed :(
Any help will be greatly appreciated!