The current version of the code doesn't support multiple solids in a single STL file, so I'm afraid you'll need to split the STL into a separate file for each solid before running the conversion. This is because the STL format itself doesn't explicitly support multiple solids. (Although an ascii STL file can be created with multiple solids, a binary STL file cannot, and I've written this code to work with both ascii and binary files.)
This works great for me with one solid, but if I have multiple solids in my .stl file, it still creates a single body in the .sat file - all the solids are lumped into one "body", but they have the correct co-ordinates etc. and are physically separate. Is this a limitation of ACIS SAT 4.0? Or does your code only ever create a single body in the .sat file?
I'm afraid I have no idea what your problem is as I have not seen the stl file you are having trouble with. However, I have updated the code to display the location of problematic facets. (The new version should be available in the next day or so.) Hope this helps you find where the problem lies.