Hi Simon,
there is a batch export script that i wrote to export multiple parts to stl format (other formats possible).
Every part you export has to have a unique name.
It doesnt change the origin befor export but this shouldnt be a big thing if you are familar with scripting MOI.

Best you follow this discussion:
http://moi3d.com/forum/index.php?webtag=MOI&msg=8582.1