Chris,
I have had that steering problem happen – what a shock when it does! I've experienced it in two different boats, one junk rig, one a small nontraditional catboat (Peep Hen microcruiser) with a gaff rig. Particular situations of light wind opposing some current seem to bring this about. The boat that I converted to junk rig never did this with the original rig, which had much less sail area. But the new junk mainsail is enormous for the boat, and in those specific situations – generally on a river, with the current going one way, and the very light breeze coming up the river in the opposite direction, with occasional eddies, the boat would completely get its own idea about where it was going to go. The solution that has worked best has been, counterintuitively, to decrease the sail area. This seems silly in such light wind – four panels, instead of the full six – but it works. With reduced sail area, the boat once again steers normally.
In the little gaff rigged boat I'm still trying to figure it out, and will have more of an opportunity this year, after the boat being out of the water for several years. In just the right conditions, that boat decides to go perpendicular to the wind and the opposing current, and heads straight for the riverbank. I have blamed this problem on the rudder, and then the problem was exacerbated by crew going forward to fend off, and being such a small boat the rudder was then lifted. But I'm assuming this would not be your problem!
Either way, what an unpleasant feeling, turning the rudder with no effect… I see that Asmat has also offered a sail-setting adjustment, so hoping that one or another approach works for you!
Shemaya