The reason this is happening is that most of your cells have been explicitly set to 'Black', while the ??? cell is set to Automatic (which also happens to be black). Excel treats this as a separate format because it's possible for a theme to apply a different color to any 'Automatic' cells.
If you look in the color filter menu, you can see that Automatic is offered as one of the three options:
You can resolve this in this case by setting the ??? cell to black instead of Automatic, but you might want to consider an alternative approach to prevent this from happening again. One option might be to use a color other than black so that there is a clear distinction between colored cells and 'automatic' cells, but conditional formatting might offer a better solution, assuming that the coloring can be logically applied based on your data.
You can see more about themes and colors in the video lesson: Essential Skills Lesson 4-8 Understand themes.
For instructions on how to apply conditional formatting, see the video tutorial: Essential Skills Lesson 4-15 Use simple conditional formatting.
I hope this explains what's been going wrong and helps you to find a good solution. Please feel free to reply if you have any further questions about this.
Jonathan is part of the professional team who answer Excel-related questions posted on the ExcelCentral.com forums.
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As well as extensive Excel knowledge, Jonathan has worked in the IT world for over thirteen years as a programmer, database designer and analyst for some of the world's largest companies.