> However when I run my transformation one of the two produces 
> the following
> saxon error:
> 
> SXXP0003: Error reported by XML parser: Document root element 
> is missing.
> 

It's actually a Xerces error: Saxon's just the messenger.

I've never worked out exactly what it means, it seems to be something of a
catch-all error to indicate that the file exists but Xerces hasn't been able
to start parsing it. I'm a little surprised that it should be produced for
an encoding problem, but it's not impossible, as it does seem to cover quite
a range of conditions.

Michael Kay
http://www.saxonica.com/