Good news everyone! I found the issue with the steam version is also an issue with the retail version and have fixed it.
Turns out the steam version gets confused and thinks that drive C is the CD-ROM resulting in more files be added to the cd emulation list - in turn re-basing the file hashes which then caused the game to think it had no files and then explode in a heap.
Hard coding drive C into the retail version caused the same crash so I could debug it with out needing steam anti anti debugger tricks
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Hopefully have a beta out some point next week.