Batch Capture Problem with 5D mark II

At the end of an event we normally copy all cards to the HDD, each card in a separate folder. We then point FCP at the card folders and use log & transfer to ingest the footage and transcode to ProRes 422.
Once all the footage is ingested we save the project and copy it from the Mac Pro to the iMac so that a second editor can work on it at the same time. Because the iMac doesn't have a RAID we set all the footage to 'offline' and use batch capture to recapture it all in ProRes Proxy.
So far so good.... that is with all the Panasonic HMC footage.... BUT we recently started shooting on the Canon 5D2 and 7D as well and this simply isn't working.
For some reason FCP recaptures all the Panasonic footage but refused to re-capture the Canon footage. I can see all the files in the L&T window but it never seems to equate the footage with the files I am trying to recapture.
HELP! What could be causing this? It's only a problem with the Canon footage.
Both MacPro and iMac are running identical versions of FCP and identical (latest) versions of the Canon L&T plug in ..... and YES we copied the entire CF card to a folder - just like we do with the Panasonic HMC stuff.

Hi Andy, compressor is current chugging away, so we'll get going for the edit I am sure. Only 600 more clips to go
I've tried everything I can think of in terms of recapturing. Even on the original Mac Pro that the footage came in to, if I copy the entire project folder (including the 'cards' folder) from one RAID to another it fails to recapture in the original project using the original codec (ProRes 422), but if I point it back to the original cards folder it works fine. It seems to be 'moving/copying' the cards that is causing the problems.
I've checked the dates and sizes on the copied files and they are all the same, and since recapturing to the original project at the original settings doesn't work once moved I am completely stumped....!

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