It seems that Refinery wrongly reports files to not exist, while they are definately there.
CHECK_file failed, file:///C:/develop/Tools/Textures/checker.tga not found
Logged In: NO
at first I had the same problems, try updating to current SVN (or via automated updater), it seems to be fixed.
Logged In: YES
It should be fixed.
Please get CoherencyTest Release (command line version) instead of using the one from Refinery.
The one from Refinery is not up to date and soon be removed.