Ok, it looks like it's the z-index of JAMasthead that's causing the issue. I was wondering about that. Changing the following seems to fix that particular problem:
/* FIX JAMASTHEAD DISABLING MAIN NAV */
.ja-masthead .ja-masthead-detail {
z-index: 0;
}
Can you let me know if this will cause any other problems?
Also, JAMasthead is still acting weird (as in, not showing up) on pages where it's explicitly called in the module settings (as per the above screenshots).
Any ideas?