Steve, I don't know if this has any thing to do with the problem your having
but I have discovered that you may have various problems with
sepatarations if you have negative numbers in your bounding box. This problem
can be fixed in Illustrator by making the lower left corner of your art the
intersection of the zeros. The bounding box measures in points and conversion
from picas to points will tell you how big your box should be. Hope this helps.
I've had alot of luck with separator so keep tryin' "Doug A."