I've updated the FAQ in question to include some extra notes/details that might be what you're running into:
[quote][ul][li]Note: This does not affect single-clicking items. Single-clicking with the middle button always toggles a file or folder's selection, like left-clicking with Ctrl held down, unless you are using Power Mode and have configured the button to do something else.[/li]
[li]Note: This does not affect virtual folders which Opus does not handle itself. Try in a generic directory like C:\ if it doesn't seem to work elsewhere.[/li]
[li]See Also: Always re-use a single window instead of opening new windows[/li]
[li]See Also: How to make Logitech Mid/Back/Forward buttons work in Opus[/li][/ul][/quote]