After several month of wondering what is going on, talking with Windows support and what else, I finally found the culprit.

There has been a really weird recurring issue where 2-3 keyboard layouts would be added to the language bar (without my doing) and those extra layouts would not appear in the language settings, meaning you can't remove them except by uninstalling all the language packs (I use three), changing the default language to a different one, and then reinstalling the ones you need. I use Bulgarian, Ancient Greek and English.

Now, this might not seem like a big deal, but when you work everyday with three languages and constantly keep switching between them, suddenly having six instead of three layouts to switch between is really inconvenient. Not to mention I don't like when programs do stuff on my PC without asking for permission.

I usually use Greek Polytonic, UK English, BGP Bulgarian Phonetic. Currently I have an additional: US United Kingdom (weird, huh), ENG United States and BGT Bulgarian Typewriter. This happened the moment I opened BibleWorks, because I recently cleaned the layouts using the above described method and hadn't opened BW yet.

Do you guys have any idea what is happening or how to prevent it? Thank you.