Or perhaps it was actually NHibernate at fault. I was trying to set up a many-to-many relationship with attributes on the association table and the ActiveRecord CreateSchema call just kept complaining that my assocation table already exists and cannot be created again.
After an hour or so of head-scatching, turns out the error only occurs when I use GUIDs as the primary key in the association table. Switching to good old "int" solved everything. I wonder if that has been fixed in the trunk, I should go code spelunking.