I can't imagine it's the thread. I've been using the same large spool of aurifil for my last three projects (and this problem never presented itself). I've re-threaded the machine a dozen times. I just discovered the last needle or two I had put in were size 90/14 quilting needles, instead of size 75/11 (which I ALWAYS use for piecing). I just sewed a few test scraps and so far it's better, but I still see bobbin thread on top (not as severe) with the upper tension on the lowest setting.
I've also tried with my previous 1/4" foot, and it's better than with the little foot. But I LOVE the little foot. The visibility is so much better that my seams are more consistent. Maybe I should just bite the bullet and tighten the bobbin tension.