Then try the betas out in a sacrificial VM first, with the software (like KM) that you need, to make sure everything you need to be productive is working before you put it in your main. Or use the beta-running VM to test your developed software.
There is no one good answer to this, I'm afraid -- running betas on a production machine is always a risk.
Totally understand -- but it was what was required to fix a beta/KM issue in this thread. So prepare yourself, in case the next update doesn't fix the problem.
Edit to add:
It would be worth checking the Engine log file, if you haven't already. Quit the Engine, run tail -f ~/Library/Logs/Keyboard\ Maestro/Engine.log in Terminal, launch the Engine again and see if anything weird shows up -- perhaps an old Library item not resolving, a macro that runs an async AppleScript querying the Engine, or similar.