bundle exec rake db:migrate -- schema.rb regenerated WITHOUT indices

I have a large database with tons of tables and many indices on those tables. Every time I run a migration, the schema.rb file is generated fine, EXCEPT none of the indices are included. New tables and columns are added fine. If I manually re-add the add_index lines to the schema.rb file after the migration, it works fine, but doing this after every migration is a major hassle.

I've been dealing with this problem for months and haven't been able to find any solution or workaround. Does anyone know what might be happening?

Using Postgres & Rails 3.