Today I have installed LanguageTools on a new computer, a clean install. I noticed that all options of the extension were available from the start and working properly.
I also tried LT version 3.4 because in my computer that was the version where I found the turned off settings.
I am still reviewing what happened and why these pre-configurations where not active on my PC install.
I am posting just to apologize to anyone that may have lost time with this, since I am unable to reproduce it on a fresh install of LibreOffice.
PS - But there is a related bug: 'Ignore All' changes settings permanently · Issue #604 · languagetool-org/languagetool · GitHub