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In order for us to be able to see the workbook, you need to post a packaged workbook (.twbx) that will include your data.
I'm guessing that you are using Measure Names/Measure Values to create your view. When you are using those, you only have one Marks Card with one Color Shelf, and unfortunately Tableau does not give us access to the members of the Measure Names/Values convenience variables to be able to apply one color to one Measure but not others. The workaround for this is to use a multiple axis crosstab, see this workbook for details:
Thanks Jonathan - this was really helpful.