Gogolo,
Ah, sorry, for some reason I thought you were using linux. The export layout file creates the shell script when you use jabref export. The shell script is really just a load of "heredocs" but I don't know what the equivalent would be in windows, or as a dos batch file. An alternative would be to write it as a python script (or other language). That would be platform independent (I think) but then would mean you would have to install python.
If you just want to do this once, you could send me the shell file that you create, I could run it and send back the manifest files in a zip file. It might be sensible to try a small number (say 50) refs first before the whole lot to make sure it works.
One other idea: I used to use jython a while back. This is python implemented in java. Presumably you have java already (to run jabref) so perhaps all that is needed is a small change to the export filter to create a python/jython script and then the jython jar file. It's a bit too late for me to get my head around this now. Another thing to add to my list for the weekend.
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