I have realised the problem which has lead to a further problem...
When working with Acrobat 6.0 and up, it writes its settings for
processing into the registry, which in the past versions used to be an
ini file in the windows directory.

What im looking for now is a way to edit the right registry files for
the writing of the file to my chosen directory, with no window being
displayed and to my chosen name.

Thanks