The color palette does not seem to work the way we think it does, unless you use global colors. I suggest you specify global colors in the swatches palette and you will have better success. Then fill your gradient with the color swatches. Notice that even though you use HSB in swatches the default name the color name R= XX G = XX B=XX. Why, because that is how illustrator codes this, as RGB values. HSB values do not get coded into the ,ai file, as HSB is really just an interface, not an actual mode that Illustrator numerically codes numbers in. for example: Select a gradient swatch in an RGB document mode .ai file, and the color pallete and shows 41% grayscale, does no mean it is filled with 41% grayscale. That is the mode we had the palette set to BEFORE we selected the swatch, and that is the approximation in grayscale. Usually the color palette mode does not switch after you select a gradient slider, but on a few occasions with your gradients it did(so I see your frustration, and cannot exactly explain this). On one occasion it say 100% grayscael, btu the color looked like a very dark grey, all I did was from the flyout menu move teh checkmark fomr grayscael to grayscale, and it got darker. Now that really bothered me, believe this is where your problem is coming from. Try switching the color palette color mode before selecting a gradient stop and most of this should begin to make sense.
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