It's not clear from your writeup what is happening when the second system call "fails". Does it actually have an error? Does it hang/timeout?

Two suggestions, to start. Both are listed in the docs for system, too. First, use the "list" form (just a good habit) and second check return values/error values -- printing these out will help you debug, too.

So: go readeth thee the docs at system again -- you say you do this, but no evidence of this exists in your code, explain more fully what the problem is (how it manifests), and let us know more about what's really going on :)