It's been a rather long discussion already, but it seems that you haven't given any of the context that precedes the "system()" line in the original post. Are you sure that the "final output file" that results from the preceding steps really exists with the expected content when 3 or more input files are involved?

How sure are you that your script isn't dying quietly at some point before "system" (and the other diagnostics you've tried now) when you have 3 or more input files?