I sincerely believe there are just situations that come up that are weird- and unexplainable. I've been fighting something simiar, with my Ruger I can shoot just was well- 9 out of 10 shots- one-handed or two. My SD? Totally different- I fire a 5-shot group and the first is a flyer, off 2-4" either left or right. the next 3 are dead on, usually almost touching- the fifth is a flyer, 2-4" either left or right, but to the opposite side of the first. Had two instructors watch, no idea what's happening- (one suggested just plain ol concentration) and with my SD I shoot much better two-handed, and the SD has a 1/2" LONGER BARREL, YOU WOULD THINK MORE ACCURATE? eVEN IF MINOR... OOps hit capslock, didn't mean to shout.
Decided it's just some mental block, at least the flyers aren't so bad I'd miss in a SD situation. And in your case, I'd say the weird difference is a blessing. I mean really- knowing a SD situation may REQUIRE one-handed shots, nice to know you're good, isn;t it. Maybe just a concentration thing with you, too, like, you try harder two-handed and it pulls you off?
Sorry, sounds like I'm rambling- the way my brain works sometimes.