Sounds like either I'm mis-remembering how it used to work (though I'm fairly certain) or the functionality has changed. Ticking a bunch of checkboxes I find to be a hassle, plus I can't see the context of each line.
IIRC the way it used to work is similar to Replace & Find within a document, except that when there are no more in the current doc, it will automatically open the next doc in the list. Worked really well and fast, although you have to kind of be aware of the silent document switch happening (can sometimes be confusing if you don't notice).
--ErikN