Why do Bundler do what it do?

A couple of notes up-front: notice that json_pure is not specifically required in my Gemfile, but it shows up with a specific version requirement in Gemfile.lock.  If that version requirement is lower than an available system version of json_pure, then this problem shows up.  I can make it show up with 1.4.4 versus 1.4.3 on my development Mac.

$ bundle --version
Bundler version 1.0.0.rc.3

$ ruby -v
ruby 1.8.7 (2010-01-10 patchlevel 249) [i686-linux]

(Not using RVM here)

$ bundle check
The Gemfile's dependencies are satisfied

$ rake -T
(in /var/www/html/cc/releases/20100807214807)
rake aborted!
You have already activated json_pure 1.4.5, but your Gemfile requires json_pure 1.4.4. Consider using bundle exec.
/var/www/html/cc/releases/20100807214807/Rakefile:4
(See full trace by running task with --trace)

$ bundle exec rake -T
/usr/local/lib/ruby/gems/1.8/gems/bundler-1.0.0.rc.3/lib/bundler/runtime.rb:27:in `setup': You have already activated json_pure 1.4.5, but your Gemfile requires json_pure 1.4.4. Consider using bundle exec. (Gem::LoadError)
	from /usr/local/lib/ruby/gems/1.8/gems/bundler-1.0.0.rc.3/lib/bundler/spec_set.rb:12:in `each'
	from /usr/local/lib/ruby/gems/1.8/gems/bundler-1.0.0.rc.3/lib/bundler/spec_set.rb:12:in `each'
	from /usr/local/lib/ruby/gems/1.8/gems/bundler-1.0.0.rc.3/lib/bundler/runtime.rb:17:in `setup'
	from /usr/local/lib/ruby/gems/1.8/gems/bundler-1.0.0.rc.3/lib/bundler.rb:95:in `setup'
	from /usr/local/lib/ruby/gems/1.8/gems/bundler-1.0.0.rc.3/lib/bundler/cli.rb:284:in `exec'
	from /usr/local/lib/ruby/gems/1.8/gems/bundler-1.0.0.rc.3/lib/bundler/vendor/thor/task.rb:22:in `send'
	from /usr/local/lib/ruby/gems/1.8/gems/bundler-1.0.0.rc.3/lib/bundler/vendor/thor/task.rb:22:in `run'
	from /usr/local/lib/ruby/gems/1.8/gems/bundler-1.0.0.rc.3/lib/bundler/vendor/thor/invocation.rb:118:in `invoke_task'
	from /usr/local/lib/ruby/gems/1.8/gems/bundler-1.0.0.rc.3/lib/bundler/vendor/thor.rb:246:in `dispatch'
	from /usr/local/lib/ruby/gems/1.8/gems/bundler-1.0.0.rc.3/lib/bundler/vendor/thor/base.rb:389:in `start'
	from /usr/local/lib/ruby/gems/1.8/gems/bundler-1.0.0.rc.3/bin/bundle:13
	from /usr/local/bin/bundle:19:in `load'
	from /usr/local/bin/bundle:19

$ cat Rakefile
# Add your own tasks in files placed in lib/tasks ending in .rake,
# for example lib/tasks/switchtower.rake, and they will automatically be available to Rake.

require(File.join(File.dirname(__FILE__), 'config', 'boot'))

require 'rake'
require 'rake/testtask'
require 'rake/rdoctask'

$ grep json Gemfile*
Gemfile.lock:      json_pure
Gemfile.lock:    json_pure (1.4.4)
Gemfile.lock:      json_pure (>= 1.1.7)

$ gem list json_pure

*** LOCAL GEMS ***

json_pure (1.4.5, 1.4.4, 1.4.0, 1.2.3, 1.2.2)

$ sudo gem uninstall json_pure --version 1.4.5
Successfully uninstalled json_pure-1.4.5

$ rake -T
(in /var/www/html/cc/releases/20100807214807)

[success]

$ bundle config
Settings are listed in order of priority. The top value will be used.

disable_shared_gems
  Set for your local app (/var/www/html/cc/releases/20100807214807/.bundle/config): "1"

without
  Set for your local app (/var/www/html/cc/releases/20100807214807/.bundle/config): ""

path
  Set for your local app (/var/www/html/cc/releases/20100807214807/.bundle/config): "vendor/bundle"

$ cat Gemfile
source :gemcutter
source "http://gems.github.com"

gem "rails", "2.3.5", :require => nil
gem "googlecharts", :require => "gchart"
gem "scruffy"
gem "builder"
gem "ferret", "~>0.11.6"
gem "google-geocode", "~>1.2"
gem "gruff"
gem "sparklines"
gem "rubyzip", :require => "zip/zip"
gem "color"
gem "pdf-writer", :require => "pdf/writer"
gem "mysql"
gem "newrelic_rpm"
gem "rmagick", "2.12.1"
gem "xml-simple", :require => "xmlsimple"
gem "spreadsheet"
gem "phone_wrangler"
gem "fastercsv"

# Needed for "rake tmp:assets:clear" to work
gem "rcov"

group :development do
  # bundler requires these gems in development
  #  gem 'rails-footnotes'
  gem "capistrano"
  gem "bullet"
end

group :test do
  # bundler requires these gems while running tests
  gem 'rspec'
  gem "nokogiri"
  gem "ZenTest", :require => nil
  gem "mocha", ">=0.9.8", :require => nil
  gem "shoulda", ">=2.11.3", :require => nil
  gem "shoulda-addons", :require => 'shoulda_addons'
  gem "webrat"
  gem "system_timer"

  gem "metric_fu", '>=1.3.0', :require => 'metric_fu'
end

group :delayed_job do
  gem 'daemon-spawn', '>=0.3.0'
end

$ cat Gemfile.lock
GEM
  remote: http://rubygems.org/
  remote: http://gems.github.com/
  specs:
    Saikuro (1.1.0)
    ZenTest (4.3.3)
    actionmailer (2.3.5)
      actionpack (= 2.3.5)
    actionpack (2.3.5)
      activesupport (= 2.3.5)
      rack (~> 1.0.0)
    activerecord (2.3.5)
      activesupport (= 2.3.5)
    activeresource (2.3.5)
      activesupport (= 2.3.5)
    activesupport (2.3.5)
    arrayfields (4.7.4)
    builder (2.1.2)
    bullet (1.7.6)
    capistrano (2.5.19)
      highline
      net-scp (>= 1.0.0)
      net-sftp (>= 2.0.0)
      net-ssh (>= 2.0.14)
      net-ssh-gateway (>= 1.0.0)
    chronic (0.2.3)
      hoe (>= 1.2.1)
    churn (0.0.12)
      chronic (~> 0.2.3)
      hirb
      json_pure
      main
      ruby_parser (~> 2.0.4)
      sexp_processor (~> 3.0.3)
    color (1.4.1)
    daemon-spawn (0.3.0)
    fastercsv (1.5.3)
    fattr (2.1.0)
    ferret (0.11.6)
      rake (> 0.0.0)
    flay (1.4.0)
      ruby_parser (~> 2.0)
      sexp_processor (~> 3.0)
    flog (2.4.0)
      ruby_parser (~> 2.0)
      sexp_processor (~> 3.0)
    google-geocode (1.2.1)
      hoe (>= 1.1.4)
      rc-rest (>= 2.0.0)
    googlecharts (1.6.0)
    gruff (0.3.6)
    highline (1.6.1)
    hirb (0.3.2)
    hoe (2.6.1)
      rake (>= 0.8.7)
      rubyforge (>= 2.0.4)
    json_pure (1.4.4)
    main (4.2.0)
      arrayfields (>= 4.7.4)
      fattr (>= 2.1.0)
    metric_fu (1.5.1)
      Saikuro (>= 1.1.0)
      activesupport (>= 2.0.0)
      chronic (>= 0.2.3)
      churn (>= 0.0.7)
      flay (>= 1.2.1)
      flog (>= 2.2.0)
      rails_best_practices (>= 0.3.16)
      rcov (>= 0.8.3.3)
      reek (>= 1.2.6)
      roodi (>= 2.1.0)
    mocha (0.9.8)
      rake
    mysql (2.8.1)
    net-http-persistent (1.2.5)
    net-scp (1.0.2)
      net-ssh (>= 1.99.1)
    net-sftp (2.0.4)
      net-ssh (>= 2.0.9)
    net-ssh (2.0.23)
    net-ssh-gateway (1.0.1)
      net-ssh (>= 1.99.1)
    newrelic_rpm (2.12.3)
    nokogiri (1.4.3.1)
    pdf-writer (1.1.8)
      color (>= 1.4.0)
      transaction-simple (~> 1.3)
    phone_wrangler (0.1.3)
    rack (1.0.1)
    rack-test (0.5.4)
      rack (>= 1.0)
    rails (2.3.5)
      actionmailer (= 2.3.5)
      actionpack (= 2.3.5)
      activerecord (= 2.3.5)
      activeresource (= 2.3.5)
      activesupport (= 2.3.5)
      rake (>= 0.8.3)
    rails_best_practices (0.3.26)
      ruby2ruby (>= 1.2.4)
      ruby_parser (>= 2.0.4)
    rake (0.8.7)
    rc-rest (4.0)
      net-http-persistent (~> 1.0)
      nokogiri (>= 1.3.1)
    rcov (0.9.8)
    reek (1.2.8)
      ruby2ruby (~> 1.2)
      ruby_parser (~> 2.0)
      sexp_processor (~> 3.0)
    rmagick (2.12.1)
    roodi (2.1.0)
      ruby_parser
    rspec (1.3.0)
    ruby-ole (1.2.10.1)
    ruby2ruby (1.2.4)
      ruby_parser (~> 2.0)
      sexp_processor (~> 3.0)
    ruby_parser (2.0.4)
      sexp_processor (~> 3.0)
    rubyforge (2.0.4)
      json_pure (>= 1.1.7)
    rubyzip (0.9.4)
    scruffy (0.2.6)
    sexp_processor (3.0.4)
    shoulda (2.11.3)
    shoulda-addons (0.2.2)
    sparklines (0.5.2)
    spreadsheet (0.6.4.1)
      ruby-ole
    system_timer (1.0)
    transaction-simple (1.4.0)
      hoe (>= 1.1.7)
    webrat (0.7.1)
      nokogiri (>= 1.2.0)
      rack (>= 1.0)
      rack-test (>= 0.5.3)
    xml-simple (1.0.12)

PLATFORMS
  ruby

DEPENDENCIES
  ZenTest
  builder
  bullet
  capistrano
  color
  daemon-spawn (>= 0.3.0)
  fastercsv
  ferret (~> 0.11.6)
  google-geocode (~> 1.2)
  googlecharts
  gruff
  metric_fu (>= 1.3.0)
  mocha (>= 0.9.8)
  mysql
  newrelic_rpm
  nokogiri
  pdf-writer
  phone_wrangler
  rails (= 2.3.5)
  rcov
  rmagick (= 2.12.1)
  rspec
  rubyzip
  scruffy
  shoulda (>= 2.11.3)
  shoulda-addons
  sparklines
  spreadsheet
  system_timer
  webrat
  xml-simple

Since google found this when I had the question, I'm providing my solution.
Check out "RUBYGEMS PLUGINS" in the man page for Bundler.
Our particular issue was gemcutter. Upgrading it fixed our issue.

Matt, thank you for the pointer! For anyone who stumbled on this later, said man page can be viewed here: http://gembundler.com/man/bundle-exec.1.html