I agree with cdarke probably no difference as the underlying OS calls are the same. However, there may be a way to change that assumption if you are using Windows NTFS. Read a bit about Wiki-NTFS and then have a look at this freeware: Ultrasearch. Microsoft may also have some updated tools itself - I couldn't find any updates to their nfi.exe tool (its an old one). Now caveat: I have not personally used this stuff and have no idea of how reliable it is! But the claim is that this thing reads the MFT (Master File Table) directly which has the potential to be a lot faster, albeit complicated and perhaps "dangerous". "Buyer beware!".

For most applications a couple of minutes is probably not that big of a deal (not worth risk and a lot of work in the quest for absolute maximum speed). I mean messing around with a big network server has the potential to cause some pretty serious damage if things go wrong! Sounds like too much pain to save a minute or so. But I leave that tradeoff to you.