I just ran into the same problem on a brand new out of the box JB unit running the 3.09.0514 OS build.  The message popped up after each reboot.  It would sometimes pop up two or three times.  In addition, I found that the Key Programmer utility would not work.  It wouldn't allow us to change the key assignments.  After performing a Factory Reset the pop up message went away and the Key Programmer started to work again. 

We have traced some, but not all, the failures, back to an incomplete update of the OS.  Some have seen the issue go away after updating the OS to the latest Jellybean version (052014).  You could try re-installing the OS to resolve the issue.

The Android Engineers state this is an internal service that sometimes fails on the first restart immediately after an OS update.  They are investigating the root cause, but the service is immediately restarted and there are no negative side effects.