For the record, drush gets very unhappy when you have drupal installs living inside each other. Luckily for me, I seem to have fixed the site, except that every. single. time. I upgrade, I have to recopy my .htaccess file back over again. I wish I knew why that happened, but it does. I could do something nutty like use teh googlez for it, but gosh, that's WORK and it's so much easier to just complain.
Look, A post I started and never posted!