I have an app that I recently updated to Rails 3.2.1 (from Rails 3.0.x) and have refactored the JS and CSS assets to make use of the new asset pipeline. Th
Although your intializer is not run when the assets are precompiling, you should still find that they run as Rails boors up as normal, however, this will be on the first hit to the application rather than at the deploy step.
I'm not entirely sure what the issue you're having is, but if you follow the Rails conventions the deploy will work as expected.