The steps listed above are no different to what install_stubby does, any issue you are facing will still persist.
The problem is with the unpredictable nat-start (and firewall-start) events which cause race conditions. I had similar issues back with Skynet a long time ago, I assumed it wouldn't be an issue with only two rules and almost no other code being executed... guess I was wrong.
I pushed
v1.0.9 which ports the Check_Lock() function from Skynet to enforce 1 instance of install_stubby at a time. This should resolve any race conditions.