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Run a query. Start going through bug list with "next". Switch to different NS window and run another query. Go back and hit next on original bug; you'll get dumped into the list for the query you made in the other window.
this is an artifact of using a cookie to hold the search results. I will look into doing away with this at some point in the future.
OK, the cookie that held the list of queried bugs has been removed. You should now be able to do multiple queries from mulitple windows without having them trample each other.