phantom missing gems caused by project iml file

I wish to report that in the "Ruby SDK and Gems"  panel of the project settings,
I had been getting the message
   "Gems required for project are not attached"  
(highlighting in red the gem versions om 1.0.0, lyber-core & rack 1.1.0),
until I manually edited the project's .iml file to remove the following lines:

    <orderEntry type="library" name="[gem] om (v1.0.0, null)" level="application" />
    <orderEntry type="library" name="[gem] lyber-core (v0.9.7.2, null)" level="application" />
    <orderEntry type="library" name="[gem] rack (v1.1.0, null)" level="application" />

These lines specified older versions of dependency gems than the ones that are currently installed by a bundle install (as verified by doing a gem list, and a review of the Gemfile and Gemfile.lock project files)

The error message persisted even after doing a "rvm gemset empty" and a fresh "bundle install", both from the command line and from the RubyMine tools menu.  It was occuring in RubyMine 3.1 release and after an upgrade to the latest EAP release.  I could not find any references to the old gem versions in my project code or anywhere else other than the project's .iml  file.   Editing that file seems to have resolved the issue, but I am curious as to how this situation might have arisen, and whether RubyMine should have cleaned up these XML elements itself.

I am using
* Mac OS X 10.6.6
* RubyMine (EAP) RM-103.170
* RVM 1.0.16
* RubyGems 1.5.2
* Bundler 1.0.10

My project has a .rvmrc file that contains
   rvm use 1.8.7@dor-gsb-robots

The "Ruby SDK and Gems"  panel showed that I have the desired ruby version and gemset selected

Tools -> Show Gem Environment   produces the following output

RubyGems Environment:
RUBY VERSION: 1.8.7 (2010-08-16 patchlevel 302) [i686-darwin10.4.0]
INSTALLATION DIRECTORY: /Users/rnanders/.rvm/gems/ruby-1.8.7-p302@dor-gsb-robots
RUBY EXECUTABLE: /Users/rnanders/.rvm/rubies/ruby-1.8.7-p302/bin/ruby
EXECUTABLE DIRECTORY: /Users/rnanders/.rvm/gems/ruby-1.8.7-p302@dor-gsb-robots/bin
   :update_sources => true
   :verbose => true
   :benchmark => false
   :backtrace => false
   :bulk_threshold => 1000
IDE: JetBrains RubyMine (EAP) RM-103.170, build #RM-103.170
RubyMine SDK Environment:
Sdk: Ruby SDK 1.8.7-p302 [dor-gsb-robots]
Sdk Version: ver.1.8.7 p302
Ruby Interpreter: /Users/rnanders/.rvm/rubies/ruby-1.8.7-p302/bin/ruby
RVM Sdk: yes, gemset:dor-gsb-robots
Sdk Language Level: 1.8
Sdk Load Path:
Sdk Gem paths:

note that there is  no ruby-1.8.7-p302@dor-gsb-robots/bundler/gems   directory on my system

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