Is it just when your starting up? one-time thing? You can try using Process Explorer from SysInternals (now owned by Microsoft) to try to view if a new program is launching just before it starts up. Unlike the normal Task Manager in Windows, Process Explorer shows which programs are opening and closing by highlighting them.
If it happens consistently, try killing programs you don't really recognize with either Task manager or process explorer until it goes away. If it only happens during startup, run msconfig from your Run dialog (press WINKEY + R), go to the startup tab, and start removing startup items and restarting until the problem goes away.
Does it look like a black command window? If so it might be a startup script that is running.