Okay so after multiple file integrity issues ("X does not exist"), I opted to install a new Matomo instance, and migrated the data from old to new. It seems to be working well and passes all system checks now. I think this can be marked resolved. I still don't know how it ever got into that state, but it's good again.

@marcusquinn Thanks Marcus!

@marcusquinn The funny thing about that is that I didn't believe the Firefox settings actually worked lol.. more like they wouldn't be honored, especially by closed source apps. Edit: @marcusquinn In that case, I'll start using it instead of Decentraleyes.

@girish Thank you! I updated and can confirm it's working as expected now with only the one LDAP server listed.

Somehow fixed by running the reset link in the plugin Settings > Support. No idea what setting was wrong but happy to confirm not a Cloudron issue. Sorry for the bother, was just eliminating possibilities. Solved. Thanks

@girish A fresh install already has it set to "No"? Interesting, I don't recall ever setting mine to "Yes", but I guess I did. Thank you for confirming, seems it's okay then if it's set to "No" by default and the cronjob is doing it automatically.