Have you uninstalled anything lately?
If it isn't a system operation, you might use msconfig.exe to check what is loading and trying to run. If you see something that might be causing such a problem, you can uncheck it to keep it from starting. If the messages stop, then that is probably the errant utility and you can tie it to the main utility.
Also, perhaps there is something in the event viewer that might help. Tie the time the message pops up to the errors or warnings (eventvwr.msc).