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