It's actually much easier to use CYGWIN from Ant than stated in the documentation with the <exec> task.  Here is an example of using Ant to run a shell script via CYGWIN (be sure the shell script is formatted for unix):
                   <exec executable="c:\cygwin\bin\bash.exe">
                     <arg value="--login"/>
                     <arg value="-c"/>
                     <arg value="/cygdrive/c/BuildDeployScripts/scp_files.sh ${scp.keyfile} ${fileToSCP} ${scp.user} ${scp.remote.host} ${scp.target.dir}"/>
                   </exec>
Note that all arguments to the script in this case must be on the same <arg> as the script file or they won't show up as args to the script, but rather, args to bash.  I haven't figured out how to send an argument with spaces in it, but I'm sure you Ant guru's could tell me.  Any help there?  I tried 'myScript.sh "argument with spaces" arg2', but that didn't work.  CYGWIN wants spaces escaped.

Thanks,
Eric