How to edit Advanced Search Form's Content Type checkbox-list using hook_form_alter
The advanced fields are added by the node.module in node_form_search_form_alter() (a hook_form_FORM_ID_alter() implementation). It sounds like your module's hook_form_alter() is getting called before the node.module one, so you're not seeing it's additions.

The ordering of when hooks are fired is controlled by the weight column in the system table. Have you altered that previously for your module? Usually, node.module has a weight of 0 so if your module comes before that in the rows in the system table when sorted by weight then that will be your problem.