(This may be different for others, and even more so for Windows 7.may be). It is located in c:\users\\local\appdata\PRX\prcctr32.exe. The file which I encountered is prcctr32.exe If you take a screenshot of the flashing command prompt window at the moment it flashes, you get to know which file is running along with its location. However, it is any help, I found one possible solution - this is specific to a Windows 8.1 update. This is perhaps now a very old problem which people may have solved.
Is this a sign of some kind of malware? I scan my computer regularly with microsoft essentials and later I switched to kaspersky, I never found any virus. Command prompt window appears and disappears, I mean it runs itself,it opens up and closes as quickly as it popped up,it happens while I surf the internet or leave the computer idle for sometime.