First of all, I plan to make a new SD image with some tweakable settings, so people can experiment with some parameters if they like. That doesn't have to do with this issue, but I think that some of the tweaks could be interesting to play with a bit.
In the meantime, I did a bit of testing myself. If I ran a SNES game just in attract mode, I didn't notice any slowdown. Then, I logged in over the network to view some things. When I would run 'top' to see the CPU usage of processes, then the game would start to stutter every once in a while. This shows that just the added overhead of networking plus 'top' is enough to slow it down.
The other thing is that lion2 mentioned that he wondered if his Pi Zero was different/defective compared to the one his friend had. That made me wonder if one was a Pi Zero and the other a Pi Zero W. If the slower one was the W, then maybe networking has something to do with it. If you want to experiment with that, you can turn off the networking of the W using these settings in the /boot/config.txt file (and reboot to make them take effect).
========
# turn wifi and bluetooth off
dtoverlay=pi3-disable-wifi
dtoverlay=pi3-disable-bt
========
So, my current thought is that you might be running a Pi Zero W that is connecting to your WiFi and then launching some background processes or something. Anyway, this still requires some more investigation, but I'd be very curious if those lines helped the problem or not.
P.S. Be careful turning off the WiFi if that's how you expect to turn it back on. Once it's off, you can't SSH back in. You'd have to connect a USB networking device or keyboard or pull the SD card and edit the file on your PC.
In the meantime, I did a bit of testing myself. If I ran a SNES game just in attract mode, I didn't notice any slowdown. Then, I logged in over the network to view some things. When I would run 'top' to see the CPU usage of processes, then the game would start to stutter every once in a while. This shows that just the added overhead of networking plus 'top' is enough to slow it down.
The other thing is that lion2 mentioned that he wondered if his Pi Zero was different/defective compared to the one his friend had. That made me wonder if one was a Pi Zero and the other a Pi Zero W. If the slower one was the W, then maybe networking has something to do with it. If you want to experiment with that, you can turn off the networking of the W using these settings in the /boot/config.txt file (and reboot to make them take effect).
========
# turn wifi and bluetooth off
dtoverlay=pi3-disable-wifi
dtoverlay=pi3-disable-bt
========
So, my current thought is that you might be running a Pi Zero W that is connecting to your WiFi and then launching some background processes or something. Anyway, this still requires some more investigation, but I'd be very curious if those lines helped the problem or not.
P.S. Be careful turning off the WiFi if that's how you expect to turn it back on. Once it's off, you can't SSH back in. You'd have to connect a USB networking device or keyboard or pull the SD card and edit the file on your PC.
Card Fighters' Clash 2 English Translation ( http://cfc2english.blogspot.com/ )
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Neo Geo Pocket Flash Cart and Linker Project ( http://www.flashmasta.com/ )
Avatar art thanks to Trev-Mun ( http://trevmun.deviantart.com/ )