In order to avoid cache-rebuilding issue one should not call entity_load() in hook_entity_info() or hook_entity_info_alter(). The same way anything else that needs entity-info should not be called, e.g. field_info_fields().
Instead of the previous work-a-round of calling entity_load() in hook_entity_info_alter() stop using entity_load() and directly query the database. With a recent entity API any exportable entities will be synced to the database already, so that should be fine.
For any releases *after* 7.x-1.0-beta11 the code in the entity API module which helps working around the entity-load() problems will be removed.