The test-touch-system-1.script I'm not sure I understand. Is it a case where your filesystem doesn't have second-granularity timestamps but only minute-granularity timestamp?
What is a good way to test that?
Further clisp bugs look like they are failures to explicitly call CMD.EXE while doing redirections. Call you add #+clisp (trace ext:shell ext:run-program uiop/run-program:%system) to test-run-program.script and run it again?
here is the output for clisp with the above trace directive in place:
https://dl.dropboxusercontent.com/u/19667598/clisp-test-3.1.0.70.text