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This is because the line separator is being converted in one case and not in the other. This seems to have been the same in 0.6.2/Qt4.
If you use Ctrl-F to select text and put it into the Find box (you don't need Ctrl-C first), then the end of line is being inserted as the unicode paragraph separator character 
. When you Ctrl-C Ctrl-V the text into the Find box, it ends up using the unicode line feed character 0a or \n. And when you actually do a search the text being compared against must be using a line feed as the separator. So in one case they match and in the other they don't.
There was a similar issue with Tokenising not picking up the paragraph separator character which was fixed. Its not clear if this is a bug in Qt that we need to work around, or a consequence of the way we get the text from the editor, or something else.
In any case, it looks like we need to automatically convert the paragraph separators into line feeds whenever we're comparing text.
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