The stuff falling through floors thing is supposedly fixed int PyFFI v2.1.9b5 according to http://sourceforge.net/tracker/index.php?func=detail&aid=3194017&group_id=199269&atid=968813.
Thanks Gratis.
As to the second part, I found the registry entry for the context menu, but I'm not quite sure how to change things so that these optimizations are called on a single file.
The current context menu can be found in:
HKEY_CLASSES_ROOT\Folder\shell\Optimize with PyFFI
and it basically just calls the niftoaster spell. I could change it to call the batch file instead, but I suspect the parameters on the niftoaster spells it calls are configured to use to in and out directories. So I guess the answer is to create a new batch file that uses the four ini files, but with the same parameters the current context menu uses...