I found a workaround using Calibre's Very nice command line app ebook-convert.exe (or drop the .exe on linux). I have Cygwin installed (I am a Very long time Unix admin so am Very comfortable there ) and used it to run a simple script I wrote that converted the broken .epub files to Calibre fixed .epubs. Very nice, quick, and easy I also modified the script to run through a directory to convert every file (with supported file extensions) to epub.

The scripts run on linux unmodified as well (I have Calibre installed on my linux server so tried it there). If anyone is interested PM me. Must have Calibre installed, and some way to run Bash (A Unix/Linux shell) scripts.