Deactivate a Gem - "you have already activated rake 0.9.3.beta.1, but my Gemfile requires rake 0.9.2"

I'm trying to run a migration but I keep getting the error message that is:

rake aborted! Undefined method prerequisite for nil:NilClass.

It seems that somehow I activated a gem called rake 0.9.3.beta.1 - however I have since changed the gem bundle install and run bundle show rake and it shows that rake 0.9.2 is installed. I'm using Git for the first time so I thought that maybe it had something to do with the application still using the beta version of rake - but I've done a push and it shows that the gemfile has been updated.

and when I look down into the gem libraries I can only see the rake 0.9.2 version. Where should I be looking?

I also have a Rails:Railtie deprecated warning - but I'm thinking that this doesn't have anything to do with my migration problems. Its telling me to use config.app_generators in config/application.rb instead of Railtie - but i can't see that in the file.

This is the Config/application.rb file

require File.expand_path('../boot', __FILE__)

# Pick the frameworks you want:
 require "active_record/railtie"
require "action_controller/railtie"
require "action_mailer/railtie"
require "active_resource/railtie"
 require "sprockets/railtie"
Bundler.require *Rails.groups(:assets) if defined?(Bundler)

module CrowdshareApp
  class Application < Rails::Application
  config.encoding = "utf-8"
config.filter_parameters += [:password]
config.assets.enabled = true
  end
end

My Gemfile looks like this:

source 'http://rubygems.org'

gem 'rails', '3.1.0.rc5'
gem 'sqlite3' 
group :assets do
  gem 'sass-rails', "~> 3.1.0.rc"
  gem 'coffee-rails', "~> 3.1.0.rc"
  gem 'uglifier'
end

gem 'jquery-rails'
group :development do
  gem   'rspec-rails', '2.0.0.beta.18'
end

group :test do
  gem 'rspec', '2.0.0.beta.18'
end

and the Gemfile.lock file has the foll