Michael,
Could you help direct me to the link in the forum regarding batch processing with MoI. You were discussing it once with a guy and I cant find it.
That was one where you would control it by generating a .js text file with a line in it for each file you wanted to convert. Then you pass that .js file as a command-line argument to moi.exe (use " " if it has spaces in it) so it will load that script and execute it when launched.
That second one had a script that would handle looping through a directory and converting all the files of a particular type it could find in there. Something like that anyway.
Let me know if what you need is not covered in either of those threads.