Occasionally, when certain programs are running/loading something in the background, they throw up a command window briefly as part of the program.. Generally, that shouldn't be happening unless there are automatic updates running for a specific program or in some cases, malware is doing something it shouldn't.

So.... you could check to see if there are any scheduled tasks running which might be causing this. (Type "Task Scheduler" in the Search/Cortana window at the bottom of the screen, open it, then select "Task Scheduler Library". Delete any you don't need.) Also check your various program installations to make sure they are installing new versions of themselves. If that's the case, then things are as they should be.

Or, just for kicks, click on the link below and follow the steps exactly to the letter to scan for spyware and malware.

“Expand” the post titled: "Please try this" at the link below:
http://www.cnet.com/forums/post/f742c795-5881-433b-a29b-6d758efe5cd3/

Hope this helps.

Grif