Hi jmayo15,
THESE STEPS SOLVED THE EXACT SAME PROBLEM FOR ME!
I just had this problem which flashes the Command Prompt in front of ur screen when is on idle or working. The famous reason for this problem to hop into your computer is malware. I had this when I downloaded random stuffs without an antivirus and malware care softwares (by disabling the windows security systems, lol). What I did was, I used Malwarebytes to solve the malware problem. Here are the steps I did :
This can help if you ONLY have CP pop up problem.
1) Download Malwarebytes (Trial Version is enough).
2) Go to 'Scan' tab and start scanning it using "Threat Scan"
3) Once done, quarantine those detected threats.
4) Go to 'Quarantine' tab in the exact same app and delete the quarantine folders.
5) Restart the computer.
6) Open the Malwarebytes and go to 'Scan' tab again and now scan using 'Hyper Scan' (as it only needs few more to detect).
7) Go to 'Quarantine' tab again and follow step 4 again.
8) Restart your PC and the problem should be gone (as for me, it did).