I ran into a bit of a mystery the other day.  I have a new rails 3 (beta3) install.  
I'm using Jeweler to build a new gem using Rake.  When I install the gem using Rake all goes along as expected.  If I go to the command line and type gem list.  My gem does not show up.  After digging around I found that the gem is getting installed into the ~/.bundler gem location.
If I run gem commands from the terminal then GEM_HOME is as I set it.
If I run gem commands from inside Rake (for my Rails 3 project that has had bundler install run on it) then it is using ~/.bundler/.. as the root of GEM_HOME.
As a result I have a gem that i need to install and re-install a lot.  So I have to execute the gem uninstall commands from inside Rake.
Here is what my rake file looks like now:
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