On custom item searches in the client, when using Does Not Equal with an item flag, search only returns results that have a flag that does n
   
    Create a custom search for items and specify that the ItemFlags.Flag Does Not Equal "something". The search will not return all items that do not have a that flag, but will return all items that have A flag but whose flag does not match "something".
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Heather Martin
    
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  Also, custom item searches for items with a specific Item flag does not display the Item flag field in the results grid. So, you can't export search results so that the items flag appears as a column in the exported spreadsheet.