Thanks Bruce.
The ICD file was the answer. I copied my ICD file to a new name, and changed LUTTransform to (8, 9, 10, 11, 12, 13, 14, 15, 0, 1, 2, 3, 4, 5, 6, 7) and now my data is ordered the way I need it.
Once I did that, I used MAX to create 2 "iid" files - one that uses the byte-swapped icd file, and the other that uses the normal icd file. Now I can select in software whether I want byte-swapped or normal data by selecting the appropriate interface.
I'm capturing 256x256 images, 16 bits per pixel, to disk at over 200 frames per second with the proper byte ordering now. I was only getting about 40 before since I was doing the byte-swap in software.
Thanks again,
Mike Gulley