Hi Alex,
First of all, this specific problem was my own doing. I was using the -4 DCRaw parm that apparently does create some issues. Some of the files that I compared with had been converted without that parm. When I removed that, DCRaw_emu worked the way I had hoped and in a very similar way to DCRaw 9.27 (but faster).

There are still a couple of small differences from DCRaw 9.27:
* Fuji X files - these are coming out with the green a sort of yellow-green. This is different from the result with DCRAW 9.27 and different from the embedded JPEG.

* The resulting file name when I convert to a Tiff file is in the format filename.raf.tiff instead of filename.tiff

Otherwise, DCRaw_emu seems to do what I need it to do.

Chris

PS: I looked on the Data Structures page for -c so that's why I couldn't find it.