This is a long-standing bug.
Mouse over Evil Omen in the buff/debuff icon, and look at the timer.
Does it say "zero seconds?"
If it says anything else, post what it says.
If it says zero seconds, what's going on isn't that you still have Evil Omen on, it's that your buff/debuff icon says you do.
To get rid of it, have Evil Omen cast upon you again, by a guildmate or a monster or a PK or something. Whenever this happens to me from PvM, I go out and fight some reds.
If this doesn't work, let us know.
-Galen's player