I have been in touch with the creator of the Mandigo theme and he reported no problems with the 2.6 - he even pointed me to a test website where it's up and running - here.
After that I've been scrutinizing my theme page and I have noted that none of the changes I make, seem to be saved when I update the options.
Also, I get an error in the theme options when I enter that area - link.
That particular line says:
in_array($page->ID, $mandigo_options['header_navigation_exclude_pages'])
And then when I scroll down to review the other options, a lot of the fields have "2" written in them - link - even if I alter this to other values and updates, the "2" returns after a refresh.
This leads me to think that WP might no be saving the information correctly.
Any help?