This is not an error with flycheck!
[Thanks to the repository owner for giving me a clear answer on that].
flycheck-phpcs-standard does not take a path to
phpcs. I had that wrong. Once I learned that, the context of the documentation made more sense.
What was happening is that Cygwin environmental path mounting is not what is running when flycheck is used.
Phpcs itself is given a unix type path
tmp/flycheck23423.buffer-copy and cannot run it. Stink me!
In response to that new, I was trying to see if I could make windows read those paths. And the good news is you can, ofcourse! This superuser QA was helpful.
This is how you fix it:
1) download the windows junction tool to a windows folder from which you will run it in cmd.exe. EDIT: see comment, should use mklink in win7.
junction \cygdrive\c \
... this will output ... Created: C:\cygdrive\c Targetted at: C:\
junction \tmp C:\cygwin\tmp
... this will output ... Created: C:\tmp Targetted at: C:\cygwin\tmp
Now, open a php script in emacs and break it. It works! It is phpcs is able to find the /tmp/.. . check it, and return the error messages. Cool.