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The index field in the info panel shows "--" on colors in my palette

If your eyedropper is set to take a merged sample (see Using the eyedropper), as is the default, and your layers have lowered opacities, overlapping colors in your layers may blend together such that the resulting color isn't in the palette. If this occurs, the index field in the info panel will show "--".

You might switch the eyedropper to only picking up colors in the active layer: that will result in the index field always being valid.

See also

Using the eyedropper
Using the info panel