How to turn off url aliases on dev site?
I think the problem is that the {url_alias} still has the aliases in it.

My suggestion would be to take a backup, then delete a few manually from "admin/build/path" (Drupal 6) or "admin/config/search/path" (Drupal 7), and then try the "node/nid" paths for the entries you deleted.  Then, take another backup :) and either delete them via the Delete aliases tab.