Menu Locations Not Copying Consistently

Hello. The site I'm working on is experiencing menu copying errors for 20% - 30% of newly created sites.

When an error occurs, it seems that the Menu Locations are not being assigned. That is, the main and footer menus are being copied, but on the Manage Locations tab, neither the main navigation menu nor the footer navigation menu have any menu assigned.

Of course, for the other 70% - 80% of sites, everything works perfectly and the menu locations are assigned.

The site is WP 3.6.1 using New Blog Templates 2.7.1. and Multi-DB is being used. WP is running on Ubuntu 12.04 with nginx and php5-fpm.

For reasons beyond my control, upgrading WP is not an option. Also, there are *many* plugins on this site, so I would like to avoid turning each one off if at all possible.

Any ideas what might be causing this/where to start looking for the problem?

Thanks for your help!