As a guess from your words, look at your action «I disabled all modules from command line».
Congratulations, you have disabled my patch too!
So, if your run module:enable after this action, the Magento 2 core bug will reproduce again (nobody patches it, you have disabled the patch by your own arms).
It is just one of my guesses from your exact words. Actually, there are plenty wrong ways to implement my 4 step upgrading instruction.