okay, nevermind, i figured it out myself.
need to hack "ob-ditaa.el":
look for the line (cmd (concat "java" .... and insert your cygwin path (e.g. c:/cygwin) just before shell-quote-argument, org-babel-process-file-name in-file and org-babel-process-file-name out-file, so that it will look like this: 

(cmd (concat "java " java " -jar c:/cygwin"
     (shell-quote-argument
      (expand-file-name org-ditaa-jar-path))
     " " cmdline
     " c:/cygwin" (org-babel-process-file-name in-file)
     " c:/cygwin" (org-babel-process-file-name out-file))))

hopefully this will help someone.

On Tue, Jan 3, 2012 at 11:05 AM, Waldemar Reusch <waldemar.reusch@googlemail.com> wrote:
http://www.mail-archive.com/emacs-orgmode@gnu.org/msg21593.html

im trying to set up ditaa on my cygwin/windows7 machine and encountered the very same problem as described in the above mentioned mail, i.e. the error "jar not accessible".
i tried to fix it by hacking org-exp-blocks, but it does not seem to make any difference. when i check the *Messages* buffer, the path to ditaa.jar is unchanged.
If anyone has this one figured out, i would appreciate your help.