As I say, I think you may need to take this up with Eizo...
There seems to be something wrong that is outside the operation of LightSpace.
What I men by "that is just wrong" is that your results are just wrong, and you probably do need Eizo's support.
With the number of Eizo/LightSpace users it seems weird that this is the only time any issues have been reported.
And seeing a difference when you upload a Bypass LUT is totally wrong!
That really can't happen, if the display was already pre-set to Null, via the Null Cube upload function (the tick box).
Seeing a change when a Bypass LUT is uploaded means the display was not set to Null before the upload.
The 'Standard' box being selected, but greyed-out, just means that display doesn't have that function.
(Not all Eizo displays do...)
But, that will not cause a Bypass LUT to show a difference when uploaded.
Are you sure you are using the Null Cube option to fully re-set the display before you profile?
Obviously, if the display has anything incorrectly set when you profile, uploading the LUT will cause a difference when compared to an Active LUT within LightSpace.
Steve
Steve Shaw
Mob Boss at Light Illusion