When you apply a mark using the Mark command, the new mark is added to existing marks.
When you mark tests through the query marking commands, the test plan editor by default clears all existing marks before running the query. Mark by Named Query supports sophisticated query combinations, and it would not make sense to retain previous marks. However, Mark by Query, which allows one-time-only queries, lets you override the default behavior and retain existing marks.
To retain existing marks, uncheck the Unmark All Before Query check box in the Mark by Query dialog box.