This article discusses the alert that can appear at the top of Menu Analysis Report for Menu Item Modifiers. This is what the alert looks like:

And this is an example of what you might see from clicking on Show Me.

What’s the fix?
Rest assured that it isn’t necessarily a problem. Each recipe row will report the correct data. It’s only in the Category Sum Totals or Sum Totals where it becomes a problem (See screenshot below). However, if that information is not important to you, then there is no need to “fix” it and you can simply ignore those rows.

For information behind the “why”, see the next section Why the Warning? Otherwise here’s the fix.
The fix is done by converting all the Menu Item Modifiers to a non-Menu Item Recipe, like Prepared Item or Bar Item recipes. Here are instructions:
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Click on the Show Me inside the alert to see all the Menu Item Modifiers.
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Create new recipes. For each Modifier Recipe in the popup, create a new Recipe under Prepared Item or Bar Item. In the example, we’d need to create a Prepared Item for Rice Recipe.
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Update PMIX Mappings. Under Accounting > PMIX Mapping, find the PMIX Item that matches the PMIX Source in the popup. In the example, we’d need to map RICE to the new Prepared Item.
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You’re done!
Why the Warning?
The Menu Analysis report is based on Menu Item Recipes. This means anything mapped to a Menu Item Recipe that is sold in that time period will show up as its own row. Below is an example.

Notice there are two rows, Chicken Recipe and Rice Recipe (with the Recipe Category is in parenthesis). The PMIX sources can be seen by clicking on the right most column’s Details. Here is the popup for Chicken Recipe.

In the modifier section you can see that the Rice Recipe modifier is showing up under Modifier costs. But wait, Rice Recipe is also its own row in the report? Remember, all Menu Item Recipes get their own row.

In this simplified example, the Rice Recipe Cost is $0.56. You can see that it is showing up under Modifier Cost of one row, and Menu Item Cost of another. But the individual rows are still reporting correct information. Indeed, it is a modifier cost and a Menu Item. But now the Sum Totals and the Category Sum Totals for Dinner Item will count the modifier cost twice. This isn’t a problem as long as you ignore those sum total rows. All other rows still contain accurate information. But if you want accurate sum total information, see Why the Warning? above.