I totally know WHY neelix does it. The problem is, he CONTINUES to do it.. like its endearing or something.. That and the fact that he keeps trying to make Tuvok laugh..
He wouldnt try that crap with Worf!... SHEEEEEEEEEEEIIIIIIIIIT
Here's where Neelix's confusion begins, immediately after getting beamed aboard.
NEELIX: Astonishing! You Federations are obviously an advanced culture.
TUVOK: The Federation is made up of many cultures. I am Vulcan.
NEELIX: Neelix. Good to meet you!
(Neelix gives Tuvok a bear hug.)
After he finally figured it out, maybe he kept using "Mr. Vulcan" as a sign of affection, or considered it an inside joke between him and Tuvok, like a nickname.
Or maybe he just liked being an @$$h*le.