The following code will create a correct HABTM relationship

User.create(:login => login, :password => 'password', :password_confirmation => 'password') do |u|
u.company = Company.first
u.admin = true
end
u = User.first
u.groups << Group.first

However the following code:

User.create(:login => login, :password => 'password', :password_confirmation => 'password') do |u|
u.company = Company.first
u.admin = true
u.groups << Group.first
end

results in the following

User.first.groups
=> [#<Group _id: 4e6d540a8625ee28d2000002, name: "test group", created_at: Mon Sep 12 00:36:26 UTC 2011, updated_at: Mon Sep 12 00:36:26 UTC 2011, user_ids: [], _type: nil, company_id: BSON::ObjectId('4e6d540a8625ee28d2000001')>]

Group.first.users
=> []