Prism tests the effectiveness of matching with an F test (distinct from the main F test of differences between columns). The matching should be part of the experimental design and not something you do after collecting data. By analyzing only the differences, therefore, a matched test controls for some of the sources of scatter. Some factors you don't control in the experiment will affect all the measurements from one subject equally, so will not affect the difference between the measurements in that subject. The whole point of using a repeated-measures test is to control for experimental variability.
Read elsewhere to learn about choosing a test, and interpreting the results. Repeated measures one-way ANOVA compares the means of three or more matched groups.
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