Hi: I’m sorry to hear you are experiencing difficulties.
In simple terms, each position in the admin menu can be described numerically (one item might live at position #5, another at position #30, etc). Occasionally two plugins/a plugin and a theme might try to register menu entries at the same position and one can therefore overwrite the other.
With that in mind, are there any differences in the activated theme/plugins between each site that might explain this? I do see when you opened this thread you noted having run through our standard troubleshooting steps already which is awesome:
YES, I’ve deactivated all other plugins to check for a plugin conflict.
YES, I’ve reverted to the 2011 default WordPress theme (with other plugins still deactivated) to check for a theme conflict.
Thanks for taking the time to do that – can you confirm if this yielded indications of any potential conflicts?