Working with windows 2003 can be somewhat awkward when running jobs via the scheduler so I was wondering if cygwin cron can be installed.  Sure enough, good old google came through with the following:

http://www.mail-archive.com/cygwin@cygwin.com/msg31579.html

The easiest way is to follow the ssh-host-config script in
creating a special account:
  net user cron_server <passwd> /add /yes
  net localgroup <administrators_group_name> cron_server /add
  editrights -a SeAssignPrimaryTokenPrivilege -u cron_server
  editrights -a SeCreateTokenPrivilege -u cron_server
  editrights -a SeIncreaseQuotaPrivilege -u cron_server
  editrights -a SeServiceLogonRight -u cron_server
  mkpasswd -l -u cron_server >> /etc/passwd
For security reasons:
  editrights -a SeDenyInteractiveLogonRight -u cron_server
  editrights -a SeDenyNetworkLogonRight -u cron_server
  editrights -a SeDenyRemoteInteractiveLogonRight -u cron_server
And then create a cron service using that account:
  cygrunsrv -I cron -p /usr/sbin/cron -a -D -u cron_server -w <passwd>