I wonder if the issue not recognising the files will be cured by editing the camera plist file as you have to do for the T2i/550D
Might be worth a go - instructions here
http://www.patience.tv/blog_files/tag-eos-550d-t2i-log-and-transfer-problem...
try adding EOS 5D Mark III to the list ?
Total guess - but might work.
best wishes
Neil
http://www.patience.tv