It appears that in adding the new conversation with Bonnie Ann when you kidnap the Major General's daughter (this appears new, as I don't recall Bonnie caring about it before, and it makes me wonder what other personality changes for her are upcoming, because I LIKE THIS!!) something happened to the conversation with the guards in the sewer before you get to that conversation.

The otter who confronts you down there uses the conversation and speech given when you turn in Captain Foote to the Sherriff in Junction. Everything else seems to be all right, though.