@weaver, thesurge appears to be right, the alignfull/wide options do not work properly with the extra menu shortcode.
Here are the results from the align options selected in the primary menu style when applied to an Extra menu
- Alignfull items right or center results in alignfull items left
- AlignWide items right or center results in alignWidew items left
Basically, it seems the Extra menu are not getting anything else than Items left for alignfull and alignwide