Replacing the Mini vMac binary with version 36.04 completely fixed the issue.

If you too have this issue and you do not want to go the compiling route, then you can simply grab the binary here and replace your /opt/retropie/emulators/minivmac/minivmac with this one : https://www.macintoshrepository.org/25178-mini-vmac-for-raspberry-pi-retropie

@hermit Looks like if you launch and exit the pixel desktop it fixes the issue. I'll try to find another workaround.

I was sure not to touch the controller on boot. I learned that lesson from the wii andI'm positive its not the controller itself that is the problem. I bought it a few days ago and it works perfectly for everything else.

I really really like the forum format and structure.
No speed issues here; using it with MBA 2011, Win10 i7 and Android .