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When querying features of a layer that intersect another layer, you may, under some circumstances, receive unexpected results.
For example, if you create a selection set for layer A, then select features from layer B that intersect features of layer (the 'Use selected features' check box is automatically checked). If you then select 'Clear selected features' from the Selection menu, no records will be selected from layer B when you click the Apply button.
'Use selected features' check box remains checked after clearing selected features. ArcMap selects records in layer B that intersect the selected features in layer A. Since there are no longer any records selected in layer A, no records are selected in layer B.
If you do not want to use selected records during the query, simply uncheck the 'Use selected features' check box.
If you have already cleared the selection, reselect the layer used to select features from the 'Features in this layer' list dropdown. This will uncheck the 'Use selected features' check box.