I am having the same issue. Outlook appears 3 times in the Start8 menu search, in fact.
1) C:\Program Files\Microsoft Office\Office15\outlook.exe (shows as "outlook")
2) C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Microsoft Office 2013\Outlook 2013 (shortcut, shows as "Outlook 2013")
3) C:\Program Files\Microsoft Office\Office15\outlook.exe (duplicate, but shows as "OUTLOOK")
I think this is a usability issue. Yes, all 3 shortcuts work, but it looks real messy and just makes you wonder why search is returning results outside of "standard libraries" even though I have the correct option set from within the start8 config. I would much prefer to restrict the results to just the start menu and nominated libraries. I wouldn't have expected to see results from my programs folder, though what is a "standard library" does not seem to be defined, so perhaps that is considered a "standard library"?.
Could you please confirm what is considered to be a standard library?
In any case, I totally agree with aggybong that we should have the option to filter out duplicate results, even if it does incur a slight delay. Or at least have some control over which libraries are included in the search results.
Despite this "bug" I have to say this is a great product. Nice work guys!