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Disable gamma baking with Separate render channels
The output difference between multi-channel .exrs and separate render channels .exrs is how the data is written, rather than a gamma application. With multi-channel .exrs, the normals (or velocity and other such elements) are written as vectors, where the X,Y and Z coordinates are numbers ranging from -1 to 1. With separate render channels, however, such vectors are written in RGB colors (0-255 for 8bit images, which corresponds to 0 to 1 in .exrs) since it goes through the 3ds Max module. It is possible to convert the colors to vectors through an Expression node in Nuke (see conversion formula here).
That wouldn't really solve anything since the effect concerns all "Separate render channels" image formats, including .vrimg (since RGB colors are expected as an output with this option), which you most likely use as an input in the vrimg2exr.exe.
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