Difference between attribute agreement analysis in the Assistant versus the Stat menu

The primary difference is the way each command defines a match in replicated experiments, where each appraiser assesses each subject multiple times. Assistant > Measurement Systems Analysis (MSA) > Attribute Agreement Analysis defines each replicate as 1 opportunity for a match. Conversely, Stat > Quality Tools > Attribute Agreement Analysis defines each set of replicates as 1 opportunity for a match.

For example, suppose each appraiser assesses each subject 3 times. If Appraiser A correctly matches the standard 2 out of 3 times for Subject A, then Stat > Quality Tools > Attribute Agreement Analysis awards Appraiser A 0 matches out of 1 opportunity assessing Subject A. But Assistant > Measurement Systems Analysis (MSA) > Attribute Agreement Analysis awards Appraiser A 2 matches out of 3 opportunities assessing Subject A.

Likewise, if Appraiser B assesses Subject B and correctly matches the standard 3 out of 3 times, then Stat > Quality Tools > Attribute Agreement Analysis awards Appraiser B 1 match out of 1 opportunity assessing Subject B. But Assistant > Measurement Systems Analysis (MSA) > Attribute Agreement Analysis awards Appraiser B 3 matches out of 3 opportunities assessing Subject B.

The different ways of counting matches may cause the same data to yield different agreement percentages, when analyzed using both commands.

Other differences exist as well:

Attribute agreement analysis in the Assistant requires binary ratings and a known standard. In the Stat menu, ratings may have more than 2 levels, may be nominal or ordinal, and a known standard is optional.
Attribute agreement analysis in the Assistant does not assess between-appraiser agreement. It only assesses agreement between each appraiser and the standard, and between all appraisers and the standard. The Stat menu offers these assessments too, plus assessment of between-appraiser agreement.
The Stat menu calculates p-values to assess the statistical significance of the observed agreement. The Assistant does not calculate p-values, but uses confidence intervals to assess the statistical significance of the observed agreement.