I have checked several times in different datasets. It looks like the function of MSA for Attribute Agreement does not work accurately
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BlueSky Statistics 10.3.2 (GA) for Windows and Mac is now available for download (See Release Notes)
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Please email (support@blueskystatistics.com) a sample dataset along with what should be the correct values you are expecting. We will verify the results and see why the discrepancy is.