Nope, I didn’t “enable the alternate widget area for the front page”.
Went ahead and rebuilt (some of ) the theme options without re-importing them; the footer and the social media in the top bar.
Don’t have an understanding yet about how WP 3.5 update messes up column mode, except that it seems to do with the import of the theme options, it can be corrected by choosing the template with the columns from the page edit itself, and it doesn’t seem to be due to the widgets selected.
Love more insight before I update my other Graphene sites (I <3 Graphene) to WP 3.5.
