Well I have to agree with checking the fuses above the battery again, when mine were badly melted I replaced just the fuse and had that same issue where the fans would not stop spinning after the car was shut off. I bypassed that fuse with a new fuse holder I bought from autozone and I haven't had any trouble since.
Here is an image of how to bypass the fuse:
It was pulled from this post:
http://forums.newbeetle.org/showthre...5&pagenumber=7