I haven't looked at this carefully, but it looks like "Find All" has incorrect behavior when it runs into source files that have changed in the background. I've noticed underlines appearing in the wrong place and got a IndexOutOfBoundsException (I think) recently, always after being prompted about a file that has changed on disk. It looks like the "find" happens on the cached file contents rather than on the new file contents.
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Corky and I briefly talked about this issue. It's possible that "Find All" discovers a file has changed and therefore puts the code to display the dialog box and to reload the file on the event queue, but then doesn't wait for a response, causing it to work with the old text, regardless of what the user decides.
I don't think we've looked at this in greater detail, though.