By your description, I wonder if they are Shimano brakes? If so, you should be sure to check that the connection where the disc mates with the hub doesn't some sort of wear problem. If it's a Shimano system, then the disc locks onto the hub similar to a cassette locking onto the freehub. If any wear is present there, then you'll need to address that. I have seen a number of these systems, and it definitely was a design flaw from Shimano. You should have your LBS take a look at it before it becomes a bigger issue.