I've been having issues with non-cask Homebrew packages getting blocked by some Gatekeeper/SIP related watchdog on my new M1 system. Stuff would just get insta-killed at load. Anyway, it seems to have been sorted now, and through identifying which packages were having the issue in Console and reinstalling them, I've resolved the issues.

Slightly educated guess: did you install the x64 emulator between when you had the problems and when they went away?

I can see brew trying to run x64 code while the emulator isn’t there blocking code from running in weird ways.

Alternatively, it might be that package updates fixed the packages that behaved incorrectly. Again, just a slightly educated guess.

I had Rosetta well before I ran into these issues, I think Homebrew still required it when I got the computer.

Before I figured out the way to identify the offending dependencies I sorted the issue through signing the executable with codesign, in a way that required me to disable part of SIP. So the code was working, it was just not being allowed to run.

Even more specifically, the only time I’ve ran into Gatekeeper is with apps that install into /Applications and have a GUI. I’ve never had this issue with stuff I only access via CLI.

You have to Ctrl+right click the app, then click Open.