I did an experiment on the site. I disabled the original JA Masthead module that came with the quick Install and created a new JA Masthead module with a few test lines of info.
This new JA Masthead module does the same as the original Masthead module. It seemed to be fine for the first few lines but when I got to about 10 lines it broke the same as the original MH module. It gives the error and then when the error goes away it will not load the Single article menu items.
I think that when the Dev guys made the change on the Single article menus to fix the navigation they might have missed connecting the JA Masthead module perhaps. This module is such an integral part of this template. If it does not work properly it is impossible to customise the look and feel to client needs.
Your most urgent assistance with this will be appreciated. I only have a few days left to get this site working.