What causes this?
Using Jamroom
This is the 'minute_maintenance' event that is queued every minute and times out at 55 seconds. If there was a serious issue your activity log would be full of these messages (one a minute). You say that you only have a few reports of this so I'm guessing that it only happens when your server is busy with other stuff and doesn't get around to this task in time.
The only module that you're likely to have installed that uses this event is the Mailer module and that is just collecting stats with it, so likely not critical to anything else, so I'd be tempted to let it go, but maybe keep an eye on it to make sure it doesn't get any worse.
hth