Our El Capitan Server was shooting off the following error messages every 30 seconds in Console.app:

mds[81]: (DiskStore.Warning:127) Failed messaging flag writer

Thinking the error might have something to do with Spotlight, I went to System Preferences->Spotlight->Privacy, and dragged my startup disk to the Privacy pane. The error messages stopped immediately.

When I removed the startup disk from the Privacy pane and allowed my trusty Mac to re-index the startup disk – the error messages began to reappear.

This machine is my server, so I’m going to leave Spotlight’s privacy enabled for all of my drives, but I’m hoping to figure out what’s wrong, later.