Unable to launch drush outside of drush folder under cygwin. Works in msysgit

Under cygwin
Cloned drush repo to /srv/www/drush. Created symlink to drush/drush in /usr/local/bin.
When I try to run drush using either the full path to drush or the symlink I receive the following output

PHP Warning:  require(/home/CJS/includes/bootstrap.inc): failed to open stream: No such file or directory in /home/CJS/C:\cygwin\srv\www\drush\drush.php on line 16
PHP Fatal error:  require(): Failed opening required '/home/CJS/includes/bootstrap.inc' (include_path='.:/php/includes') in /home/CJS/C:\cygwin\srv\www\drush\drush.php on line 16

If I change the symlink in usr/local/bin to reference drush.php the issue resolves itself.
I am able to run drush under msysgit using either drush script or drush.php.

After looking through the drush script it appears this is the following code is the cause of the issue:

if [ -n "$CYGWIN" ] ; then
  SCRIPT_PATH="`cygpath -w -a -- "$SCRIPT_PATH"`"
fi

Specifically -w which is creating Windows style names. After replace -w with -u to create Unix style names the issue resolved itself. This change has does not affect the functionality of the drush script under msysgit.

I've attached a patch with my change.