Re-reading over all the steps herein, I can’t explain it!
The Blinkt! uses “bitbanged” IO, which means the GPIO pins are toggled independently by program code in much the same way as you might toggle an LED. Just a little faster!
It could be that they’re damaged in such a way that they don’t produce a reliable high-speed signal, even with the pins being toggled on and off, but there’s no easy way to test that if you don’t have an oscilloscope handy.
It might be worth grabbing the latest Blinkt! library since I’ve fixed some timing issues that could explain why a Pi 3B+ doesn’t work while a Zero does. On your Pi 3:
sudo pip install blinkt
And see what happens.