Apparently I was a tad too enthousiast about the fixed errors in WP-Supercache 0.9.6.1. Users are reporting sudden 404 errors for the homepage and other articles in 0.9.6.1. This was already reported to me when I upgraded to 0.9.6, but I forgot to mention this since I already downgraded to 0.9.5 due to the other (fixed) errors.
I'm at loss why the 404 errors suddenly pop up for our homepage or published articles. Has this been reported by others as well?