I had this issue too. I had a child header file where I had simply moved the navigation from above to below the banner image but the mobile menu was not working.
I tried the plugin reset but it didnt work. I copied the header file from the main 2012 them to the child theme, made the edit again and it worked ok. This fixed the two sites I have using 2012.
I have not examined the code but must be a difference somewhere between 2012 them v1.4 and 1.5 or possibly 3.9 and 4.0 of WP as I did not notice the issue until recently.