It's an interesting proposition. I always applaud somebody who's eager to think outside the box and try something new.
As has been mentioned, I think the issue lies with rationality serving as the trump card. I'm reminded of the movie Boogeyman starring Barry Watson, where the protagonist keeps reminding himself, "Don't be scared...don't be scared..." because if he can face the fear, the boogeyman can't get him.
One thing that I thought might be interesting is to really play up the psychological aspect. You could use some layered versions of reality, akin to the way that Richard Kelly does in his movie Donnie Darko or the way that Ken Kesey did in One Flew over the Cuckoo's Nest Neil Gaiman's Neverwhere is another example of how two separate levels of reality can coexist.
I think a device like you're suggesting would be more effective if the reader can't always guess which layer of reality the characters are encountering.
I think you could also play up on the fear/paranoia aspect.
Example: Poor Jake beleives in magic and the occult and whatnot. This leads to his being drained by a vampire. The police, rational guardians of rational people living in a ::rational:: society find a human corpse drained of blood. Word leaks out to the press. People begin to talk. They jump at shadows or hang garlic cloves over their doors. This paranoia leads to a self-fulfilling prophecy of somebody else dying, and the paranoia of vampires grows even more...
I dunno if either of those ideas tickle your fancy at all. However you decide to run with it, good luck.