I'm pretty sure it does. Have you killed the monster in one hit, i.e. was it still slowed when you finished it? Probably it also doesn't count when your mana shield deals the killing blow, but I'm not sure about this part.
pouzzler wrote:(I use the windows steam version under Wine, mainly because I didn't want to start over when the linux version got released, in case it could be the cause of this peculiarity, which I doubt)
You won't lose your progress if you've got a DD.net account synced up - just log in on both versions and it'll share your saves