Spotlight acting up - files/folders not found after a few minutes after a reboot

Since a few days ago Spotlight (no changes on the system as far as I remember) has been acting up: when I reboot, everything works fine. Then, after a few minutes some files/folders can't be found anymore (Alfred shows "Waiting for results...", Spotlight just shows everything but files/folders). Give it a few more minutes and another search and no files/folders can be found. For some reason, Applications, Bookmarks & History, and Notes are always searchable.

To make it even more confusing, I left the Mac running for an hour after Spotlight was showing indexing progress, came back to it - and it works. And then in a minute it doesn't work again.

I tried rebuilding the index, a few times. Ran every command I found on any forum that people said solved their Spotlight indexing issues. Fixed disk permissions. Ran maintenance scripts, etc. etc.

I'm running out of ideas. I'd probably assume it has to be hitting an issue after I run a search and that breaks it but I've no idea how to check or confirm that.