Sounds like justification is applied prior to hyphenation (it would almost have to be, to determine if the line is too long).
It might be fixable, but would probably not be pretty to code.
I leave the details to the author's reply.
It is (from a coding standpoint) similar to the not justifing and hypenating of the last line of the page.
What do you do with any over-flow if that is the last page of the document?