@cbeams OK, turns out it wasn't fixed - back to short logout times. Very strange, some software designers really don't seem to think this sort of thing is an issue, clearly over absorbed in their own ideas and under appreciative of users.
@d19dotca Yeah, I get what you're saying. The process is not that bad though. As long as you keep the same settings, it's a drop and drop of the files and hitting the start button. It'll save them to the folder you had specified on a previous run and you'll be doing two things as once, resizing and crunching (less work for the server).
For what it's worth, if this helps at all, I have always logged in with the default admin account but then set my LDAP user as a super admin, then logged out and logged back in as the LDAP user and as a super admin I removed the default admin account. That way I effectively replace the default admin account with my own LDAP user.
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. 🙂
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.
@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.