Original 5D Mark iii H264 to Color Issues

Ive cut a project in Final Cut using ProRes422 Files created in Log and Transfer.
ive now reconformed the final edit back to the original 5d3 H264 files ready to grade in color.
The problem is once its in Color (via send to color) all the edits are wrong, ie the clips are all out of sync and referencing another segment of that peice of footage.
I know that reconforming back to H264 does work as ive done it on 60D and 5D Mark ii with no issues at all. but the mark 3 is a different kettle of fish.
id prefer to grade the H264 rather than the prores.
any one had this issue and know a fix? (other than grading prores)
details of footage if it helps: 1080P 25fps IPB compression
Thanks for any help

Strange becuase ive graded H264 files from 60D and 5D2 many times in color without the need for ProRes until final render from color. ive only started having issues with the 5D3. (of course when editing i cut with prores proxy files)
>If you are going to use Color, you need to grade ProRes.  Besides, ProRes is 10-bit 4:2:2...the original H.263 files are 8-bit 4:2:0
This is true but you lose data everytime you transcode and prores likes to compress blacks ive found. from my own experience ive have better results grading H264 files in color.
Ive very fimilar witht the 5D/prores workflow as thats how i used to do it but once i found i have more flexiblity using the h264 ive always used that.... until i got a 5d3

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