I added debug lines to a cron file of mine, and honestly sometimes it isn't even being called. Sometimes when it's called, the XenForo_Error::logError isn't being processed (no errors/debug lines being logged).
Right now, the cron isn't running at all. It's set to run every minute, I've tried running it manually. It ran about half a time and hasn't ran since.
In addition to this not working, the trophy cron isn't running either.
So really, they run at random times by the looks of it and seem to skip over lines, somehow?