[v0id]

Your problem is that your parameters to the system-function are directed to sh (of Cygwin). sh does not recognize "pause" nor "cls" as those are not a part of the Cygwin-package (or Unix). I can't say why that is, and I have like I said never experienced it, or heard about others having the same problem.

You could try opening "cmd(.exe)" and compile and run it by-hand, and see what the result then is, without using Cygwin.